R News

CHANGES IN R-devel

SIGNIFICANT USER-VISIBLE CHANGES

Serialization format version 3 becomes the default for
serialization and saving of the workspace (save(),
serialize(), saveRDS(), compiler::cmpfile()).
Serialized data in format 3 cannot be read by versions of R prior
to version 3.5.0. Serialization format version 2 is still
supported and can be selected by version = 2 in the
save/serialization functions. The default can be changed back for
the whole R session by setting environment variables
R_DEFAULT_SAVE_VERSION and R_DEFAULT_SERIALIZE_VERSION
to 2. For maximal back-compatibility, files
‘vignette.rds’ and ‘partial.rdb’ generated by R
CMD build are in serialization format version 2, and resave by
default produces files in serialization format version 2 (unless
the original is already in format version 3).

NEW FEATURES

Sys.setFileTime() has been vectorized so arguments
path and time of length greater than one are now
supported.

axis() gets new option gap.axis = NA for
specifying a multiplication factor for the minimal “gap”
(distance) between axis labels drawn. Its default is 1
for labels parallel to the axis, and 0.25 for
perpendicular ones.

There is a new function, nullfile(), to give the file
name of the null system device (e.g., ‘/dev/null’) on the
current platform.

There are two new options, keep.parse.data and
keep.parse.data.pkgs, which control whether parse data are
included into sources when keep.source or
keep.source.pkgs is TRUE. By default,
keep.parse.data.pkgs is now FALSE, which changes
previous behavior and significantly reduces space and time overhead
when sources are kept when installing packages.

In rapply(x, ..), x can also be
“list-like” and of length >= 2^{31}.

trimws() gets new optional whitespace
argument, allowing more extensive definitions of “space”,
such as including Unicode spaces (as wished in PR#17431).

weighted.mean() no longer coerces the weights to a
double/numeric vector, since sum() now handles integer
overflow. This makes weighted.mean() more polymorphic and
endomorphic, but be aware that the results are no longer
guaranteed to be a vector of type double.

compiler::cmpfile() gains a version argument, for
use when the output file should be saved in serialization format 2.

The axis labeling in the default method of pairs()
may now be toggled by new options horOdd and verOdd.

(Not Windows nor macOS.) Package tcltk now supports an
environment variable R_DONT_USE_TK which if set disables Tk
initialization. This is intended for use to circumvent errors in
loading the package, e.g. with recent Linux running under
an address sanitizer.

The numeric method of all.equal() gets
optional arguments countEQ and formatFUN. If
countEQ is true, the mean error is more sensible when many
entries are equal.

vcov(<mlm>) is more efficient via new optional
arguments in summary.mlm().

The default method of summary() gets an option to
choose the kind of quantile()s to use; wish of
PR#17438.

Fitting multiple linear models vialm() does
work with matrix offsets, as suggested in PR#17407.

The new functions mem.maxVSize() and
mem.maxMSize() allow the maximal size of the vector heap
and the maximal number of nodes allowed in the current R
process to be queried and set.

news() gains support for ‘NEWS.md’ files.

An effort has been started to have our reference manuals,
i.e., all help pages. show platform-independent information (rather
than Windows or Unix-alike specifics visible only on that platform).
Consequently, the Windows version of X11() / x11()
got identical formal arguments to the Unix one.

sessionInfo()$running has been factored out in a new
variable osVersion.

slice.index() now also works for multi-dimensional
margins.

untar() used with an external tar command
assumes this supports decompression including xz and
automagically detecting the compression type. This has been true
of all mainstream implementations since 2009 (for GNU
tar, since version 1.22): older implementations are
still supported via the new argument
support_old_tars whose default is controlled by environment
variable R_SUPPORT_OLD_TARS. (It looks like NetBSD and
OpenBSD have ‘older’ tar commands for this
purpose.)

The new function asplit() allow splitting an array or
matrix by its margins.

New functions errorCondition() and
warningCondition() provide a convenient way to create
structured error and warning objects.

.Deprecated() now signals a warning of class
"deprecatedWarning", and .Defunct() now signals an
error of class "defunctError".

Many ‘package not found’ errors are now signaled as
errors of class "packageNotFoundError".

As an experimental feature, when loadNamespace() fails
because the requested package is not available the error is
initially signaled with a retry_loadNamespace restart
available. This allows a calling handler to try to install the
package and continue.

S3method() directives in ‘NAMESPACE’ can now
also be used to perform delayed S3 method registration.

Experimentally, setting environment variable
_R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors
if the variable is set to a ‘true’ value) when && or
|| encounter and use arguments of length more than one.

Added "lines" and "chars" coordinate systems
to grconvertX() and grconvertY().

getOption() is more efficient notably for the rare
case when called with two arguments, from several contributors in
PR#17394.

In .col(dim) and .row(dim), dim now may
also be an integer valued "double".

sQuote() and dQuote() get an explicit q
argument with obvious default instead of using
getOption("fancyQuotes") implicitly and unconditionally.

unzip() can list archives with comments and with
spaces in file names even using an external unzip command.

Command line completion has a new setting
rc.settings(dots = FALSE) to remove ... from the
list of possible function arguments.

library() no longer checks packages with compiled
code match R.version$platform. loadNamespace()
never has, and increasingly the ‘canonical name’ does not
reflect the important characteristics of compiled code.

The primitive functions drop and unclass now
avoid duplicating their data for atomic vectors that are large
enough by returning ALTREP wrapper objects with adjusted
attributes. R-level assignments to change attributes will also
use wrapper objects to avoid duplicating data for larger atomic
vectors. R functions like structure and unname will
therefore not duplicate data in these settings. Generic vectors as
produced by list are not yet covered by this optimization
but may be in due course.

In formals(), envir becomes an optional
argument instead of being hardwired.

INSTALLATION on a UNIX-ALIKE

The C++ compiler defaults to the C++11 standard if
supported, otherwise to the C++98 standard.

UTILITIES

R CMD check now optionally checks makefiles for
correct and portable use of the SHLIB_OPENMP_*FLAGS macros.

R CMD check now evaluates \Sexpr{}
expressions (including those in macros) before checking the
contents of ‘Rd’ files and so detects issues both in
evaluating the expressions and in the expanded contents.

R CMD check now lists missing packages separated
by commas and with regular quotes such as to be useful as argument
in calling install.packages(c(..)); from a suggestion by
Marcel Ramos.

TESTING

The random number generator tests in
‘tests/p-r-random-tests.R’ no longer fail occasionally as
they now randomly sample from “certified” random seeds.

DEPRECATED AND DEFUNCT

Argument compressed of untar() is
deprecated — it is only used for external tar commands
which increasingly for extraction auto-detect compression and
ignore their zjJ flags.

var(f) and hence sd(f) now give an error for
factor arguments; they gave a warning since R 3.2.3,
PR#16564.

tools' vignetteDepends() has been deprecated
(it called a function deprecated since Feb 2016), partly replaced
by newly exported vignetteInfo().

BUG FIXES

drop1.glm miscalculated the score test (test="Rao")
when the model contained an offset.

replayPlot(r) now also works in the same R session
when r has been “reproduced” from serialization,
typically after saving to and reading from an RDS file.

substr() and substring() now signal an error
when the input is invalid UTF-8.

file.copy() now works also when its argument to
is of length greater than one.

The documentation for identify() incorrectly claimed
that the indices of identified points were returned in the order
that the points were selected.. identify() now has a new
argument order to allow the return value to include the
order in which points were identified; the documentation has been
updated. Reported by Richard Rowe and Samuel Granjeaud.

order(...., decreasing=c(TRUE,FALSE)) could fail in
some cases. Reported from StackOverflow via Karl Nordström.

Calling install.packages() with a length zero
pkgs argument now is a no-op (PR#17422).

unlist(x) now returns a correct factor when
x is a nested list with factor leaves, fixing PR#12572
and PR#17419.

The documentation help(family) gives more details
about the aic component, thanks to Ben Bolker's prompting.

The documentation for attributes and
`attributes<-` now gives x as name of the first and
main argument which the implementation has been requiring, fixing
PR#17434. For consistency, the first argument name is also
changed from obj to x for `mostattributes<-`.

The print() method for "htest" objects now
formats the test statistic and parameter directly and hence no
longer rounds to units before the decimal point. Consequently,
printing of t.test() results with a small number of digits
now shows non-large df's to the full precision (PR#17444).

kruskal.test() and fligner.test() no longer
erroneously insist on numeric g group arguments (PR#16719).

Printing a news db via the browser now does a much better
job (PR#17433).

print.aov() missed column names in the multivariate case
due to misspelling (reported by Chris Andrews).

axis() now creates valid at locations also for
small subnormal number ranges in log scale plots.

format.POSIXlt() now also recycles the zone
and gmtoff list components to full length when needed,
and its internal C code detects have_zone in more cases.
In some cases, this changes its output to become compatible with
format.POSIXct().

On Windows, detectCores() now detects processors in all
processor groups, not just the group R is running in (impacts
particularly systems with more than 64 logical processors). Reported
by Arunkumar Srinivasan.

On Windows, socketSelect() would hang with more than
64 sockets, and hence parallel::clusterApplyLB() would hang
with more than 64 workers. Reported by Arunkumar Srinivasan.

Using \Sexpr[stage=install]{..} to create an
‘Rd’ section no longer gives a warning in R CMD
check; problem originally posted by Gábor Csárdi, then reported
as PR#17479 with a partial patch by Duncan Murdoch.

Parse data now include a special node for equal assignment.

split.default() no longer relies on [[<-(), so
it behaves as expected when splitting an object by a factor with
the empty string as one of its levels. Thanks to Brad Friedman for
the report.

Line numbers in messages about ‘.Rd’ files are now more
reliable, thanks to a patch from Duncan Murdoch.

In the numeric method for all.equal(), a
numeric scale argument is now checked to be positive and
allowed to be of length > 1. (The latter worked originally and
with a warning in recent years).

Deferred string conversions now record the OutDec
option setting when not equal to the default. Reported by Michael
Sannella.

When y is numeric and f a factor,
plot(y ~ f) nicely uses "y" and "f" as y- and x-labels.
The more direct boxplot(y ~ f) now does too. New
ann = FALSE may be used to suppress these.

Subassignment to no/empty rows of a data frame now is more
consistent and typically a no-op in all cases instead of sometimes
an error; part of Emil Bode's PR#17483.

Calls like formatC(*, zero.print = "< 0.001") no
longer give an error and are further improved via new optional
argument replace.zero. Reported by David Hugh-Jones.

formalArgs("<fn>") now finds the same function as
formals(*), fixing Emil Bode's PR#17499.

CHANGES IN R 3.5.1 patched

BUG FIXES

vcov(<empty mlm>) and hence confint() now
work (via a consistency change in summary.lm()).

confint(<multiple lm()>) now works correctly;
reported on R-devel by Steven Pav.

quade.test() now also works correctly when its
arguments are not yet sorted along groups, fixing PR#15842.

Installation on a Unix-alike tries harder to link to the
pthread library where required (rather than relying on
OpenMP to provide it: configuring with --disable-openmp
was failing on some Linux systems).

The data.frame method for print(x) is fast now
also for large data frames x and got an optional argument
max, thanks to suggestions by Juan Telleria.

untar() ignored a character compressed
argument: however many external tar programs ignore
the flags which should have been set and automagically choose the
compression type, and if appropriate gzip or
bzip2 compression would have been chosen from the magic
header of the tarball.

zapsmall(x) now works for more “number-like” objects.

The tools-internal function called from R CMD
INSTALL now gets a warnOption = 1 argument and only sets
options(warn = warnOption) when that increases the warning
level (PR#17453).

Analogously, the tools-internal function called from R CMD
check gets a warnOption = 1 argument and uses the larger
of that and getOption("warn"), also allowing to be run with
increased warning level.

Unbuffered connections now work with encoding conversion.
Reported by Stephen Berman.

‘.Renviron’ on Windows with Rgui is again by
default searched for in user documents directory when invoked
via the launcher icon. Reported by Jeroen Ooms.

printCoefmat() now also works with explicit
right=TRUE.

print.noquote() now also works with explicit
quote=FALSE.

The default method for pairs(.., horInd=*, verInd=*)
now gets the correct order, thanks to reports by Chris Andrews and
Gerrit Eichner. Additionally, when horInd or verInd
contain only a subset of variables, all the axes are labeled
correctly now.

agrep("..|..", .., fixed=FALSE) now matches when it
should, thanks to a reminder by Andreas Kolter.

str(ch) now works for more invalid multibyte strings.

CHANGES IN R 3.5.0

SIGNIFICANT USER-VISIBLE CHANGES

All packages are by default byte-compiled on installation.
This makes the installed packages larger (usually marginally so)
and may affect the format of messages and tracebacks (which often
exclude .Call and similar).

NEW FEATURES

factor() now uses order() to sort its levels,
rather than sort.list(). This allows factor() to
support custom vector-like objects if methods for the appropriate
generics are defined. It has the side effect of making
factor() succeed on empty or length-one non-atomic
vector(-like) types (e.g., "list"), where it failed before.

chooseCRANmirror() and chooseBioCmirror() no
longer have a useHTTPS argument, not needed now all R
builds support https:// downloads.

New summary() method for warnings() with a
(somewhat experimental) print() method.

(methods package.) .self is now automatically
registered as a global variable when registering a reference class
method.

tempdir(check = TRUE) recreates the tempdir()
directory if it is no longer valid (e.g. because some
other process has cleaned up the ‘/tmp’ directory).

New askYesNo() function and "askYesNo" option
to ask the user binary response questions in a customizable but
consistent way. (Suggestion of PR#17242.)

New low level utilities ...elt(n) and ...length()
for working with ... parts inside a function.

isTRUE() is more tolerant and now true
in

x <- rlnorm(99)
isTRUE(median(x) == quantile(x)["50%"])

New function isFALSE() defined analogously to isTRUE().

The default symbol table size has been increased from 4119
to 49157; this may improve the performance of symbol resolution
when many packages are loaded. (Suggested by Jim Hester.)

line() gets a new option iter = 1.

Reading from connections in text mode is buffered,
significantly improving the performance of readLines(), as
well as scan() and read.table(), at least when
specifying colClasses.

order() is smarter about picking a default sort
method when its arguments are objects.

available.packages() has two new arguments which
control if the values from the per-session repository cache are
used (default true, as before) and if so how old cached values can
be used (default one hour).

These arguments can be passed from install.packages(),
update.packages() and functions calling that: to enable
this available.packages(), packageStatus() and
download.file() gain a ... argument.

packageStatus()'s upgrade() method no longer
ignores its ... argument but passes it to
install.packages().

installed.packages() gains a ... argument to
allow arguments (including noCache) to be passed from
new.packages(), old.packages(),
update.packages() and packageStatus().

factor(x, levels, labels) now allows duplicated
labels (not duplicated levels!). Hence you can map
different values of x to the same level directly.

Attempting to use names<-() on an S4 derivative of a
basic type no longer emits a warning.

The list method of within() gains an option
keepAttrs = FALSE for some speed-up.

system() and system2() now allow the
specification of a maximum elapsed time (‘timeout’).

debug() supports debugging of methods on any object
of S4 class "genericFunction", including group generics.

Attempting to increase the length of a variable containing
NULL using length()<- still has no effect on the
target variable, but now triggers a warning.

lower.tri(x) and upper.tri(x) only needing
dim(x) now work via new functions .row() and
.col(), so no longer call as.matrix() by default in
order to work efficiently for all kind of matrix-like objects.

print() methods for "xgettext" and
"xngettext" now use encodeString() which keeps,
e.g. "\n", visible. (Wish of PR#17298.)

package.skeleton() gains an optional encoding
argument.

approx(), spline(), splinefun() and
approxfun() also work for long vectors.

deparse() and dump() are more useful for S4
objects, dput() now using the same internal C code instead
of its previous imperfect workaround R code. S4 objects now
typically deparse perfectly, i.e., can be recreated identically
from deparsed code.

dput(), deparse() and dump() now print the
names() information only once, using the more readable
(tag = value) syntax, notably for list()s, i.e.,
including data frames.

These functions gain a new control option "niceNames" (see
.deparseOpts()), which when set (as by default) also uses
the (tag = value) syntax for atomic vectors. On the other
hand, without deparse options "showAttributes" and
"niceNames", names are no longer shown also for lists.
as.character(list( c (one = 1))) now includes the name, as
as.character(list(list(one = 1))) has always done.

m:n now also deparses nicely when m > n.

The "quoteExpressions" option, also part of "all",
no longer quote()s formulas as that may not re-parse
identically. (PR#17378)

If the option setWidthOnResize is set and TRUE,
R run in a terminal using a recent readline library will
set the width option when the terminal is
resized. Suggested by Ralf Goertz.

If multiple on.exit() expressions are set using
add = TRUE then all expressions will now be run even if one
signals an error.

The character methods for as.Date() and
as.POSIXlt() are more flexible via new arguments
tryFormats and optional: see their help pages.

on.exit() gains an optional argument after
with default TRUE. Using after = FALSE with
add = TRUE adds an exit expression before any
existing ones. This way the expressions are run in a first-in
last-out fashion. (From Lionel Henry.)

On Windows, file.rename() internally retries the
operation in case of error to attempt to recover from possible
anti-virus interference.

Command line completion on :: now also includes
lazy-loaded data.

If the TZ environment variable is set when date-time
functions are first used, it is recorded as the session default
and so will be used rather than the default deduced from the OS
if TZ is subsequently unset.

There is now a [ method for class "DLLInfoList".

glm() and glm.fit get the same
singular.ok = TRUE argument that lm() has had
forever. As a consequence, in glm(*, method = <your_own>),
user specified methods need to accept a singular.ok
argument as well.

aspell() gains a filter for Markdown (‘.md’ and
‘.Rmd’) files.

intToUtf8(multiple = FALSE) gains an argument to
allow surrogate pairs to be interpreted.

The maximum number of DLLs that can be loaded into R
e.g. viadyn.load() has been increased up to 614
when the OS limit on the number of open files allows.

Sys.timezone() on a Unix-alike caches the value at
first use in a session: inter alia this means that setting
TZ later in the session affects only the current time
zone and not the system one.

Sys.timezone() is now used to find the system timezone to
pass to the code used when R is configured with
--with-internal-tzcode.

When tar() is used with an external command which is
detected to be GNU tar or libarchive tar (aka
bsdtar), a different command-line is generated to
circumvent line-length limits in the shell.

system(*, intern = FALSE), system2() (when not
capturing output), file.edit() and file.show() now
issue a warning when the external command cannot be executed.

The “default” ("lm" etc) methods of
vcov() have gained new optional argument complete =
TRUE which makes the vcov() methods more consistent with
the coef() methods in the case of singular designs. The
former (back-compatible) behavior is given by vcov(*,
complete = FALSE).

New function getDefaultCluster() in package
parallel to get the default cluster set via
setDefaultCluster().

str(x) for atomic objects x now treats both
cases of is.vector(x) similarly, and hence much less often
prints "atomic". This is a slight non-back-compatible
change producing typically both more informative and shorter
output.

gc() gets new argument full.

write.dcf() gets optional argument useBytes.

New, partly experimental packageDate() which tries to
get a valid "Date" object from a package ‘DESCRIPTION’
file, thanks to suggestions in PR#17324.

tools::resaveRdaFiles() gains a version
argument, for use when packages should remain compatible with
earlier versions of R.

ar.yw(x) and hence by default ar(x) now work
when x has NAs, mostly thanks to a patch by Pavel
Krivitsky in PR#17366. The ar.yw.default()'s AIC
computations have become more efficient by using
determinant().

New warnErrList() utility (from package nlme,
improved).

By default the (arbitrary) signs of the loadings from
princomp() are chosen so the first element is non-negative.

If --default-packages is not used, then
Rscript now checks the environment variable
R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes
precedence over R_DEFAULT_PACKAGES. If default packages are
not specified on the command line or by one of these environment
variables, then Rscript now uses the same default
packages as R. For now, the previous behavior of not
including methods can be restored by setting the environment
variable R_SCRIPT_LEGACY to yes.

When a package is found more than once, the warning from
find.package(*, verbose=TRUE) lists all library locations.

POSIXt objects can now also be rounded or truncated to month
or year.

stopifnot() can be used alternatively via new argument
exprs which is nicer and useful when testing several
expressions in one call.

The environment variable R_MAX_VSIZE can now be used
to specify the maximal vector heap size. On macOS, unless specified
by this environment variable, the maximal vector heap size is set to
the maximum of 16GB and the available physical memory. This is to
avoid having the R process killed when macOS over-commits
memory.

sum(x) and sum(x1,x2,..,x<N>) with many or
long logical or integer vectors no longer overflows (and returns
NA with a warning), but returns double numbers in
such cases.

Single components of "POSIXlt" objects can now be
extracted and replaced via [ indexing with 2 indices.

S3 method lookup now searches the namespace registry after
the top level environment of the calling environment.

Arithmetic sequences created by 1:n,
seq_along, and the like now use compact internal
representations via the ALTREP framework. Coercing integer
and numeric vectors to character also now uses the ALTREP
framework to defer the actual conversion until first use.

Finalizers are now run with interrupts suspended.

merge() gains new option no.dups and by
default suffixes the second of two duplicated column names,
thanks to a proposal by Scott Ritchie (and Gabe Becker).

scale.default(x, center, scale) now also allows
center or scale to be “numeric-alike”, i.e.,
such that as.numeric(.) coerces them correctly. This also
eliminates a wrong error message in such cases.

par*apply and par*applyLB gain an optional
argument chunk.size which allows to specify the granularity of
scheduling.

Some as.data.frame() methods, notably the
matrix one, are now more careful in not accepting
duplicated or NA row names, and by default produce unique
non-NA row names. This is based on new function
.rowNamesDF(x, make.names = *) <- rNms where the logical
argument make.names allows to specify how invalid
row names rNms are handled. .rowNamesDF() is a
“workaround” compatible default.

R has new serialization format (version 3) which supports
custom serialization of ALTREP framework objects. These
objects can still be serialized in format 2, but less efficiently.
Serialization format 3 also records the current native encoding of
unflagged strings and converts them when de-serialized in R
running under different native encoding. Format 3 comes with new
serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be
selected by version = 3 in save(),
serialize() and saveRDS(), but format 2 remains the
default for all serialization and saving of the workspace.
Serialized data in format 3 cannot be read by versions of R prior
to version 3.5.0.

The "Date" and “date-time” classes
"POSIXlt" and "POSIXct" now have a working
length<-() method, as wished in PR#17387.

optim(*, control = list(warn.1d.NelderMead = FALSE))
allows to turn off the warning when applying the default
"Nelder-Mead" method to 1-dimensional problems.

matplot(.., panel.first = .) etc now work, as
log becomes explicit argument and ... is passed to
plot() unevaluated, as suggested by Sebastian Meyer in PR#17386.

Interrupts can be suspended while evaluating an expression
using suspendInterrupts. Subexpression can be evaluated
with interrupts enabled using allowInterrupts. These
functions can be used to make sure cleanup handlers cannot be
interrupted.

R 3.5.0 includes a framework that allows packages to
provide alternate representations of basic R objects
(ALTREP). The framework is still experimental and may
undergo changes in future R releases as more experience is
gained. For now, documentation is provided in
https://svn.r-project.org/R/branches/ALTREP/ALTREP.html.

UTILITIES

install.packages() for source packages now has the
possibility to set a ‘timeout’ (elapsed-time limit). For
serial installs this uses the timeout argument of
system2(): for parallel installs it requires the
timeout utility command from GNU coreutils.

It is now possible to set ‘timeouts’ (elapsed-time
limits) for most parts of R CMD checkvia
environment variables documented in the ‘R Internals’
manual.

The ‘BioC extra’ repository which was dropped from
Bioconductor 3.6 and later has been removed from
setRepositories(). This changes the mapping for 6–8 used
by setRepositories(ind=).

R CMD check now also applies the settings of
environment variables _R_CHECK_SUGGESTS_ONLY_ and
_R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes.

R CMD check with environment variable
_R_CHECK_DEPENDS_ONLY_ set to a true value makes
test-suite-management packages available and (for the time being)
works around a common omission of rmarkdown from the
VignetteBuilder field.

INSTALLATION on a UNIX-ALIKE

Support for a system Java on macOS has been
removed — install a fairly recent Oracle Java (see ‘R
Installation and Administration’ §C.3.2).

configure works harder to set additional flags in
SAFE_FFLAGS only where necessary, and to use flags which
have little or no effect on performance.

In rare circumstances it may be necessary to override the
setting of SAFE_FFLAGS.

C99 functions expm1, hypot, log1p and
nearbyint are now required.

configure sets a -std flag for the C++
compiler for all supported C++ standards (e.g., -std=gnu++11
for the C++11 compiler). Previously this was not done in a few
cases where the default standard passed the tests made
(e.g. clang 6.0.0 for C++11).

C-LEVEL FACILITIES

‘Writing R Extensions’ documents macros
MAYBE_REFERENCED, MAYBE_SHARED and
MARK_NOT_MUTABLE that should be used by package C
code instead NAMED or SET_NAMED.

The object header layout has been changed to support merging
the ALTREP branch. This requires re-installing packages
that use compiled code.

NAMEDMAX has been raised to 3 to allow protection of
intermediate results from (usually ill-advised) assignments in
arguments to BUILTIN functions. Package C code using
SET_NAMED may need to be revised.

DEPRECATED AND DEFUNCT

Sys.timezone(location = FALSE) is defunct, and is
ignored (with a warning).

methods:::bind_activation() is defunct now; it
typically has been unneeded for years.

The undocumented ‘hidden’ objects .__H__.cbind and
.__H__.rbind in package base are deprecated (in
favour of cbind and rbind).

The declaration of pythag() in ‘Rmath.h’ has
been removed — the entry point has not been provided since R
2.14.0.

BUG FIXES

printCoefmat() now also works without column names.

The S4 methods on Ops() for the "structure" class no
longer cause infinite recursion when the structure is not an S4 object.

nlm(f, ..) for the case where f() has a
"hessian" attribute now computes
LL' = H + µI correctly. (PR#17249).

An S4 method that “rematches” to its generic and
overrides the default value of a generic formal argument to
NULL no longer drops the argument from its formals.

Rscript can now accept more than one argument given on
the #! line of a script. Previously, one could only pass a
single argument on the #! line in Linux.

Connections are now written correctly with encoding
"UTF-16LE". (PR#16737).

Evaluation of ..0 now signals an error. When
..1 is used and ... is empty, the error message is
more appropriate.

(Windows mainly.) Unicode code points which require
surrogate pairs in UTF-16 are now handled. All systems should
properly handle surrogate pairs, even those systems that do not
need to make use of them. (PR#16098)

stopifnot(e, e2, ...) now evaluates the
expressions sequentially and in case of an error or warning shows
the relevant expression instead of the full stopifnot(..)
call.

path.expand() on Windows now accepts paths specified as
UTF-8-encoded character strings even if not representable in the
current locale. (PR#17120)

line(x, y) now correctly computes the medians of the
left and right group's x-values and in all cases reproduces
straight lines.

Extending S4 classes with slots corresponding to special
attributes like dim and dimnames now works.

Fix for legend() when fill has multiple values
the first of which is NA (all colours used to default to
par(fg)). (PR#17288)

installed.packages() did not remove the cached value
for a library tree that had been emptied (but would not use the
old value, just waste time checking it).

The documentation for installed.packages(noCache = TRUE)
incorrectly claimed it would refresh the cache.

aggregate(<data.frame>) no longer uses spurious names
in some cases. (PR#17283)

object.size() now also works for long vectors.

packageDescription() tries harder to solve
re-encoding issues, notably seen in some Windows locales. This
fixes the citation() issue in PR#17291.

poly(<matrix>, 3) now works, thanks to prompting by
Marc Schwartz.

readLines() no longer segfaults on very large files
with embedded '\0' (aka ‘nul’) characters.
(PR#17311)

ns() (package splines) now also works for a
single observation. interpSpline() gives a more friendly
error message when the number of points is less than four.

dist(x, method = "canberra") now uses the correct
definition; the result may only differ when x contains
values of differing signs, e.g. not for 0-1 data.

Arithmetic with zero-column data frames now works more
consistently; issue raised by Bill Dunlap.

Arithmetic with data frames gives a data frame for ^ (which
previously gave a numeric matrix).

pretty(x, n) for large n or large
diff(range(x)) now works better (though
it was never meant for large n); internally it uses the
same rounding fuzz (1e-10) as seq.default() — as it did up
to 2010-02-03 when both were 1e-7.

Internal C-level R_check_class_and_super() and hence
R_check_class_etc() now also consider non-direct super
classes and hence return a match in more cases. This e.g., fixes
behaviour of derived classes in package Matrix.

as.matrix(dd) now works when the data frame dd
contains a column which is a data frame or matrix, including a
0-column matrix/d.f. .

mclapply(X, mc.cores) now follows its documentation
and calls lapply() in case mc.cores = 1 also in the
case mc.preschedule is false. (PR#17373)

aggregate(<data.frame>, drop=FALSE) no longer calls
the function on <empty> parts but sets corresponding results to
NA. (Thanks to Suharto Anggono's patches in PR#17280).

The duplicated() method for data frames is now based
on the list method (instead of string coercion). Consequently
unique() is better distinguishing data frame rows, fixing
PR#17369 and PR#17381. The methods for matrices and arrays
are changed accordingly.

Calling names() on an S4 object derived from
"environment" behaves (by default) like calling
names() on an ordinary environment.

read.table() with a non-default separator now
supports quotes following a non-whitespace character, matching the
behavior of scan().

parLapplyLB and parSapplyLB have been fixed to do
load balancing (dynamic scheduling). This also means that results of
computations depending on random number generators will now really be
non-reproducible, as documented.

Deparsing of consecutive ! calls is now consistent
with deparsing unary - and + calls and creates code
that can be reparsed exactly; thanks to a patch by Lionel Henry in
PR#17397. (As a side effect, this uses fewer parentheses in
some other deparsing involving ! calls.)

CHANGES IN R 3.4.4

NEW FEATURES

Sys.timezone() tries more heuristics on Unix-alikes and so
is more likely to succeed (especially on Linux). For the slowest
method, a warning is given recommending that TZ is set to
avoid the search.

The version of LAPACK included in the sources has been
updated to 3.8.0 (for the routines used by R, a very minor bug-fix
change).

parallel::detectCores(logical = FALSE) is ignored on
Linux systems, since the information is not available with
virtualized OSes.

INSTALLATION on a UNIX-ALIKE

configure will use pkg-config to find the
flags to link to jpeg if available (as it should be for the
recently-released jpeg-9c and libjpeg-turbo). (This
amends the code added in R 3.3.0 as the module name in
jpeg-9c is not what that tested for.)

DEPRECATED AND DEFUNCT

Sys.timezone(location = FALSE) (which was a stop-gap
measure for Windows long ago) is deprecated. It no longer returns
the value of environment variable TZ (usually a location).

Legacy support of make macros such as CXX1X
is formally deprecated: use the CXX11 forms instead.

BUG FIXES

power.prop.test() now warns when it cannot solve the
problem, typically because of impossible constraints. (PR#17345)

R CMD INSTALL now correctly sets C++ compiler flags
when all source files are in sub-directories of ‘src’.

CHANGES IN R 3.4.3

INSTALLATION on a UNIX-ALIKE

A workaround has been added for the changes in location of
time-zone files in macOS 10.13 ‘High Sierra’ and
again in 10.13.1, so the default time zone is deduced
correctly from the system setting when R is configured with
--with-internal-tzcode (the default on macOS).

R CMD javareconf has been updated to recognize the
use of a Java 9 SDK on macOS.

BUG FIXES

intToUtf8() converts integers corresponding to
surrogate code points to NA rather than invalid UTF-8, as
well as values larger than the current Unicode maximum of
0x10FFFF. (This aligns with the current RFC3629.)

Fix calling of methods on S4 generics that dispatch on
... when the call contains ....

Following Unicode ‘Corrigendum 9’, the UTF-8
representations of U+FFFE and U+FFFF are now regarded as valid by
utf8ToInt().

UTILITIES

INSTALLATION on a UNIX-ALIKE

The order of selection of OpenMP flags has been changed:
Oracle Developer Studio 12.5 accepts -fopenmp and
-xopenmp but only the latter enables OpenMP so it is now
tried first.

BUG FIXES

within(List, rm(x1, x2)) works correctly again,
including when List[["x2"]] is NULL.

regexec(pattern, text, *) now applies
as.character(.) to its first two arguments, as documented.

write.table() and related functions,
writeLines(), and perhaps other functions writing text to
connections did not signal errors when the writes failed,
e.g. due to a disk being full. Errors will now be
signalled if detected during the write, warnings if detected when
the connection is closed. (PR#17243)

model.matrix(~1, mf) now gets the row names from
mf also when they differ from 1:nrow(mf), fixing
PR#14992 thanks to the suggestion by Sebastian Meyer.

sigma(fm) now takes the correct denominator degrees
of freedom for a fitted model with NA coefficients. (PR#17313)

hist(x, "FD") no longer “dies” with a somewhat
cryptic error message when x has extreme outliers or
IQR() zero: nclass.FD(x) tries harder to find a
robust bin width h in the latter case, and
hist.default(*, breaks) now checks and corrects a too large
breaks number. (PR#17274)

callNextMethod() works for ... methods.

qr.coef(qd, y) now has correct names also when
qd is a complex QR or stems from qr(*, LAPACK=TRUE).

Setting options(device = *) to an invalid function no
longer segfaults when plotting is initiated. (PR#15883)

array(character(), 1) now gives (a 1D array with)
NA as has been documented for a long time as in the other
cases of zero-length array initialization and also compatibly with
matrix(character(), *). As mentioned there, this also
fixes PR#17333.

splineDesign(.., derivs = 4) no longer segfaults.

fisher.test(*, hybrid=TRUE) now (again) will use the
hybrid method when Cochran's conditions are met, fixing PR#16654.

CHANGES IN R 3.4.1

INSTALLATION on a UNIX-ALIKE

The deprecated support for PCRE versions older than 8.20
has been removed.

parse() no longer gives spurious warnings when
extracting srcrefs from a file not encoded in the current locale.

This was seen from R CMD check with ‘inst/doc/*.R’
files, and check has some additional protection for such files.

print.noquote(x) now always returns its argument
x (invisibly).

Non-UTF-8 multibyte character sets were not handled properly
in source references. (PR#16732)

CHANGES IN R 3.4.0

SIGNIFICANT USER-VISIBLE CHANGES

(Unix-alike)
The default methods for download.file() and url()
now choose "libcurl" except for file://
URLs. There will be small changes in the format and wording of
messages, including in rare cases if an issue is a warning or an
error. For example, when HTTP re-direction occurs, some messages
refer to the final URL rather than the specified one.

Those who use proxies should check that their settings are
compatible (see ?download.file: the most commonly used
forms work for both "internal" and "libcurl").

table() has been amended to be more internally
consistent and become back compatible to R<= 2.7.2
again. Consequently, table(1:2, exclude = NULL) no longer
contains a zero count for <NA>, but useNA = "always"
continues to do so.

summary.default() no longer rounds, but its print
method does resulting in less extraneous rounding, notably of
numbers in the ten thousands.

factor(x, exclude = L) behaves more rationally when
x or L are character vectors. Further,
exclude = <factor> now behaves as documented for long.

Arithmetic between length-1 arrays and longer non-arrays had
silently dropped the array attributes and recycled. This now
gives a warning and will signal an error in the future, as it has
always for logic and comparison operations in these cases (e.g.,
compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).

The JIT (‘Just In Time’) byte-code compiler is now
enabled by default at its level 3. This means functions will be
compiled on first or second use and top-level loops will be
compiled and then run. (Thanks to Tomas Kalibera for extensive
work to make this possible.)

For now, the compiler will not compile code containing explicit
calls to browser(): this is to support single stepping from
the browser() call.

JIT compilation can be disabled for the rest of the session using
compiler::enableJIT(0) or by setting environment variable
R_ENABLE_JIT to 0.

xtabs() works more consistently with NAs, also
in its result no longer setting them to 0. Further, a new
logical option addNA allows to count NAs where
appropriate. Additionally, for the case sparse = TRUE, the
result's dimnames are identical to the default case's.

Matrix products now consistently bypass BLAS when the inputs
have NaN/Inf values. Performance of the check of
inputs has been improved. Performance when BLAS is used is
improved for matrix/vector and vector/matrix multiplication (DGEMV
is now used instead of DGEMM).

One can now choose from alternative matrix product implementations
viaoptions(matprod = ). The "internal"
implementation is not optimized for speed but consistent in
precision with other summations in R (using long double
accumulators where available). "blas" calls BLAS directly
for best speed, but usually with undefined behavior for inputs
with NaN/Inf.

NEW FEATURES

User errors such as integrate(f, 0:1, 2) are now caught.

Add signature argument to debug(),
debugonce(), undebug() and isdebugged() for
more conveniently debugging S3 and S4 methods. (Based on a patch by
Gabe Becker.)

Add utils::debugcall() and
utils::undebugcall() for debugging the function that would
be called by evaluating the given expression. When the call is to
an S4 generic or standard S3 generic, debugcall() debugs the
method that would be dispatched. A number of internal utilities
were added to support this, most notably
utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.)

Add utils::strcapture(). Given a character vector and
a regular expression containing capture expressions,
strcapture() will extract the captured tokens into a
tabular data structure, typically a data.frame.

str() and strOptions() get a new option
drop.deparse.attr with improved but changed default
behaviour for expressions. For expression objects
x, str(x) now may remove extraneous white space and
truncate long lines.

str(<looooooooong_string>) is no longer very slow;
inspired by Mikko Korpela's proposal in PR#16527.

str(x)'s default method is more “accurate” and
hence somewhat more generous in displaying character vectors; this
will occasionally change R outputs (and need changes to some
‘*.Rout(.save)’ files).
For a classed integer vector such as x <- xtabs(~ c(1,9,9,9)),
str(x) now shows both the class and "int", instead
of only the latter.

isSymmetric(m) is much faster for large asymmetric
matrices mvia pre-tests and a new option tol1
(with which strict back compatibility is possible but not the
default).

The result of eigen() now is of class "eigen"
in the default case when eigenvectors are computed.

After seven years of deprecation, duplicated factor levels
now produce a warning when printed and an error in levels<-
instead of a warning.

Invalid factors, e.g., with duplicated levels (invalid but
constructable) now give a warning when printed, via new
function .valid.factor().

sessionInfo() has been updated for Apple's change in
OS naming as from ‘10.12’ (‘macOS Sierra’ vs
‘OS X El Capitan’).

Its toLatex() method now includes the running
component.

options(interrupt=) can be used to specify a default
action for user interrupts. For now, if this option is not set
and the error option is set, then an unhandled user
interrupt invokes the error option. (This may be dropped in
the future as interrupt conditions are not error
conditions.)

In most cases user interrupt handlers will be called with a
"resume" restart available. Handlers can invoke this
restart to resume computation. At the browser prompt the r
command will invoke a "resume" restart if one is
available. Some read operations cannot be resumed properly when
interrupted and do not provide a "resume" restart.

Radix sort is now chosen by method = "auto" for
sort.int() for double vectors (and hence used for
sort() for unclassed double vectors), excluding
‘long’ vectors.

sort.int(method = "radix") no longer rounds double vectors.

The default and data.frame methods for
stack() preserve the names of empty elements in the levels
of the ind column of the return value. Set the new
drop argument to TRUE for the previous behavior.

Speedup in simplify2array() and hence sapply() and
mapply() (for the case of names and common length > 1),
thanks to Suharto Anggono's PR#17118.

table(x, exclude = NULL) now sets
useNA = "ifany" (instead of "always").
Together with the bug fixes for this case, this recovers more
consistent behaviour compatible to older versions of R. As
a consequence, summary() for a logical vector no longer
reports (zero) counts for NA when there are no NAs.

dump.frames() gets a new option
include.GlobalEnv which allows to also dump the global
environment, thanks to Andreas Kersting's proposal in PR#17116.

system.time() now uses message() instead of
cat() when terminated early, such that
suppressMessages() has an effect; suggested by Ben Bolker.

try() gains a new argument outFile with a
default that can be modified viaoptions(try.outFile = .), useful notably for Sweave.

The unexported low-level functions in package parallel
for passing serialized R objects to and from forked children now
support long vectors on 64-bit platforms. This removes some
limits on higher-level functions such as mclapply() (but
returning gigabyte results from forked processes via
serialization should be avoided if at all possible).

Connections now print() without error even if
invalid, e.g. after having been destroyed.

apropos() and find(simple.words = FALSE) no
longer match object names starting with . which are known
to be internal objects (such as .__S3MethodsTable__.).

Convenience function hasName() has been added; it
is intended to replace the common idiom !is.null(x$name)
without the usually unintended partial name matching.

source() gets new optional arguments, notably
exprs; this is made use of in the new utility function
withAutoprint().

sys.source() gets a new toplevel.env argument.
This argument is useful for frameworks running package tests;
contributed by Tomas Kalibera.

Sys.setFileTime() and
file.copy(copy.date = TRUE) will set timestamps with
fractions of seconds on platforms/filesystems which support this.

(Windows only.) file.info() now returns file
timestamps including fractions of seconds; it has done so on other
platforms since R 2.14.0. (NB: some filesystems do not
record modification and access timestamps to sub-second
resolution.)

The license check enabled by
options(checkPackageLicense = TRUE) is now done when the
package's namespace is first loaded.

ppr() and supsmu() get an optional
trace argument, and ppr(.., sm.method = ..spline) is
no longer limited to sample size n <= 2500.

The POSIXct method for print() gets optional
tz and usetz arguments, thanks to a report from
Jennifer S. Lyon.

Package tools now exports function
CRAN_package_db() for obtaining information about current
packages in the CRAN package repository, and several
functions for obtaining the check status of these packages.

The (default) Stangle driver Rtangle allows
annotate to be a function and gets a new
drop.evalFALSE option.

The default method for quantile(x, prob) should now
be monotone in prob, even in border cases, see PR#16672.

bug.report() now tries to extract an email address
from a BugReports field, and if there is none, from a
Contacts field.

The format() and print() methods for
object.size() results get new options standard and
digits; notably, standard = "IEC" and
standard = "SI" allow more standard (but less common)
abbreviations than the default ones, e.g. for kilobytes.
(From contributions by Henrik Bengtsson.)

If a reference class has a validity method,
validObject will be called automatically from the
default initialization method for reference classes.

read.dcf() now consistently interprets any
‘whitespace’ to be stripped to include newlines.

The maximum number of DLLs that can be loaded into R
e.g. viadyn.load() can now be increased by
setting the environment variable R_MAX_NUM_DLLS before
starting R.

Assigning to an element of a vector beyond the current
length now over-allocates by a small fraction. The new vector is
marked internally as growable, and the true length of the new
vector is stored in the truelength field. This makes
building up a vector result by assigning to the next element
beyond the current length more efficient, though pre-allocating is
still preferred. The implementation is subject to change and not
intended to be used in packages at this time.

Loading the parallel package namespace no longer sets
or changes the .Random.seed, even if R_PARALLEL_PORT
is unset.

NB: This can break reproducibility of output, and did for a
CRAN package.

Methods "wget" and "curl" for
download.file() now give an R error rather than a non-zero
return value when the external command has a non-zero status.

Encoding name "utf8" is mapped to "UTF-8".
Many implementations of iconv accept "utf8", but not
GNU libiconv (including the late 2016 version 1.15).

sessionInfo() shows the full paths to the library or
executable files providing the BLAS/LAPACK implementations
currently in use (not available on Windows).

The binning algorithm used by bandwidth selectors
bw.ucv(), bw.bcv() and bw.SJ() switches to a
version linear in the input size n for n > nb/2.
(The calculations are the same, but for larger n/nb it is
worth doing the binning in advance.)

There is a new option PCRE_study which controls when
grep(perl = TRUE) and friends ‘study’ the compiled
pattern. Previously this was done for 11 or more input strings:
it now defaults to 10 or more (but most examples need many more
for the difference from studying to be noticeable).

grep(perl = TRUE) and friends can now make use of
PCRE's Just-In-Time mechanism, for PCRE >= 8.20 on
platforms where JIT is supported. It is used by default whenever
the pattern is studied (see the previous item). (Based on
a patch from Mikko Korpela.)

This is controlled by a new option PCRE_use_JIT.

Note that in general this makes little difference to the speed,
and may take a little longer: its benefits are most evident on
strings of thousands of characters. As a side effect it reduces
the chances of C stack overflow in the PCRE library on very long
strings (millions of characters, but see next item).

Warning: segfaults were seen using PCRE with JIT enabled on 64-bit
Sparc builds.

There is a new option PCRE_limit_recursion for
grep(perl = TRUE) and friends to set a recursion limit
taking into account R's estimate of the remaining C stack space
(or 10000 if that is not available). This reduces the chance of C
stack overflow, but because it is conservative may report a
non-match (with a warning) in examples that matched before. By
default it is enabled if any input string has 1000 or more bytes.
(PR#16757)

There is a new argument onIdle for
getGraphicsEvent(), which allows an R function to be run
whenever there are no pending graphics events. This is currently
only supported on X11 devices. Thanks to Frederick Eaton.

The deriv() and similar functions now can compute
derivatives of log1p(), sinpi() and similar
one-argument functions, thanks to a contribution by Jerry Lewis.

median() gains a formal ... argument, so
methods with extra arguments can be provided.

strwrap() reduces indent if it is more than
half width rather than giving an error. (Suggested by Bill
Dunlap.)

When the condition code in if(.) or
while(.) is not of length one, an error instead of a
warning may be triggered by setting an environment variable, see
the help page.

Formatting and printing of bibliography entries
(bibentry) is more flexible and better documented. Apart
from setting options(citation.bibtex.max = 99) you can also
use print(<citation>, bibtex=TRUE) (or format(..))
to get the BibTeX entries in the case of more than one entry.
This also affects citation().
Contributions to enable style = "html+bibtex" are welcome.

C-LEVEL FACILITIES

Entry points R_MakeExternalPtrFn and
R_ExternalPtrFn are now declared in header
‘Rinternals.h’ to facilitate creating and retrieving an R
external pointer from a C function pointer without ISO C warnings
about the conversion of function pointers.

There was an exception for the native Solaris C++ compiler
to the dropping (in R 3.3.0) of legacy C++ headers from headers
such as ‘R.h’ and ‘Rmath.h’ — this has now been
removed. That compiler has strict C++98 compliance hence does not
include extensions in its (non-legacy) C++ headers: some
packages will need to request C++11 or replace non-C++98 calls
such as lgamma: see §1.6.4 of ‘Writing R Extensions’.

Because it is needed by about 70 CRAN packages, headers ‘R.h’
and ‘Rmath.h’ still declare

use namespace std;

when included on Solaris.

When included from C++, the R headers now use forms such as
std::FILE directly rather than including the line

Headers for Unix-only facilities ‘R_ext/GetX11Image.h’,
‘R_ext/QuartzDevice.h’ and ‘R_ext/eventloop.h’ are no
longer installed on Windows.

No-longer-installed headers ‘GraphicsBase.h’,
‘RGraphics.h’, ‘Rmodules/RX11.h’ and
‘Rmodules/Rlapack.h’ which had a LGPL license no longer do so.

HAVE_UINTPTR_T is now defined where appropriate by
Rconfig.h so that it can be included before
Rinterface.h when CSTACK_DEFNS is defined and a C
compiler (not C++) is in use. Rinterface.h now includes C
header ‘stdint.h’ or C++11 header ‘cstdint’ where
needed.

Package tools has a new function
package_native_routine_registration_skeleton() to assist
adding native-symbol registration to a package. See its help and
§5.4.1 of ‘Writing R Extensions’ for how to use it. (At
the time it was added it successfully automated adding
registration to over 90% of CRAN packages which lacked
it. Many of the failures were newly-detected bugs in the
packages, e.g. 50 packages called entry points with varying
numbers of arguments and 65 packages called entry points not in
the package.)

INSTALLATION on a UNIX-ALIKE

readline headers (and not just the library) are
required unless configuring with --with-readline=no.

configure now adds a compiler switch for C++11
code, even if the compiler supports C++11 by default. (This
ensures that g++ 6.x uses C++11 mode and not its default
mode of C++14 with ‘GNU extensions’.)

The tests for C++11 compliance are now much more comprehensive.
For gcc < 4.8, the tests from R 3.3.0 are used in order to maintain
the same behaviour on Linux distributions with long-term support.

An alternative compiler for C++11 is now specified with
CXX11, not CXX1X. Likewise C++11 flags are specified
with CXX11FLAGS and the standard (e.g., -std=gnu++11)
is specified with CXX11STD.

configure now tests for a C++14-compliant compiler
by testing some basic features. This by default tries flags for
the compiler specified by CXX11, but an alternative compiler,
options and standard can be specified by variables CXX14,
CXX14FLAGS and CXX14STD (e.g., -std=gnu++14).

There is a new macro CXXSTD to help specify the
standard for C++ code, e.g. -std=c++98. This
makes it easier to work with compilers which default to a later
standard: for example, with CXX=g++6 CXXSTD=-std=c++98configure will select commands for g++ 6.x
which conform to C++11 and C++14 where specified but otherwise use
C++98.

Support for the defunct IRIX and OSF/1 OSes and Alpha CPU
has been removed.

configure checks that the compiler specified by
$CXX $CXXFLAGS is able to compile C++ code.

configure checks for the required header
‘sys/select.h’ (or ‘sys/time.h’ on legacy systems) and
system call select and aborts if they are not found.

If available, the POSIX 2008 system call utimensat
will be used by Sys.setFileTime() and
file.copy(copy.date = TRUE). This may result in slightly
more accurate file times. (It is available on Linux and FreeBSD
but not macOS.)

The minimum version requirement for libcurl has been
reduced to 7.22.0, although at least 7.28.0 is preferred and
earlier versions are little tested. (This is to support Debian 7
‘Wheezy’ LTS and Ubuntu ‘Precise’ 12.04 LTS,
although the latter is close to end-of-life.)

configure tests for a C++17-compliant compiler.
The tests are experimental and subject to change in the future.

INCLUDED SOFTWARE

(Windows only) Tcl/Tk version 8.6.4 is now included in the
binary builds. The ‘tcltk*.chm’ help file is no longer
included; please consult the online help at
http://www.tcl.tk/man/ instead.

The version of LAPACK included in the sources has been
updated to 3.7.0: no new routines have been added to R.

PACKAGE INSTALLATION

There is support for compiling C++14 or C++17 code in
packages on suitable platforms: see ‘Writing R Extensions’
for how to request this.

The order of flags when LinkingTo other packages has
been changed so their include directories come earlier, before
those specified in CPPFLAGS. This will only have an effect
if non-system include directories are included with -I
flags in CPPFLAGS (and so not the default
-I/usr/local/include which is treated as a system include
directory on most platforms).

Packages which register native routines for .C or
.Fortran need to be re-installed for this version (unless
installed with R-devel SVN revision r72375 or later).

Make variables with names containing CXX1X are
deprecated in favour of those using CXX11, but for the time
being are still made available via file
‘etc/Makeconf’. Packages using them should be converted to
the new forms and made dependent on R (>= 3.4.0).

It now knows about all the variables used for the C++98, C++11 and
C++14 standards.

R CMD check now checks that output files in
‘inst/doc’ are newer than the source files in ‘vignettes’.

For consistency with other package subdirectories, files
named ‘*.r’ in the ‘tests’ directory are now recognized
as tests by R CMD check. (Wish of PR#17143.)

R CMD build and R CMD check now use the
union of R_LIBS and .libPaths(). They may not
be equivalent, e.g., when the latter is determined by
R_PROFILE.

R CMD build now preserves dates when it copies files
in preparing the tarball. (Previously on Windows it changed the
dates on all files; on Unix, it changed some dates when installing
vignettes.)

The new option R CMD check --no-stop-on-test-error
allows running the remaining tests (under ‘tests/’) even if
one gave an error.

Check customization via environment variables to
detect side effects of .Call() and .External() calls
which alter their arguments is described in §8 of the ‘R
Internals’ manual.

R CMD check now checks any BugReports field
to be non-empty and a suitable single URL.

R CMD check --as-cran now NOTEs if the package
does not register its native routines or does not declare its
intentions on (native) symbol search. (This will become a WARNING
in due course.)

DEPRECATED AND DEFUNCT

(Windows only) Function setInternet2() is defunct.

Installation support for readline emulations based on
editline (aka libedit) is deprecated.

Use of the C/C++ macro NO_C_HEADERS is defunct and
silently ignored.

unix.time(), a traditional synonym for
system.time(), has been deprecated.

structure(NULL, ..) is now deprecated as you cannot
set attributes on NULL.

Header ‘Rconfig.h’ no longer defines
SUPPORT_OPENMP; instead use _OPENMP (as documented
for a long time).

(C-level Native routine registration.) The deprecated
styles member of the R_CMethodDef and
R_FortranMethodDef structures has been removed.
Packages using these will need to be re-installed for R 3.4.0.

The deprecated support for PCRE versions older than 8.20
will be removed in R 3.4.1. (Versions 8.20–8.31 will still be
accepted but remain deprecated.)

BUG FIXES

Getting or setting body() or formals() on
non-functions for now signals a warning and may become an error
for setting.

match(x, t), duplicated(x) and
unique(x) work as documented for complex numbers with NAs
or NaNs, where all those containing NA do match,
whereas in the case of NaN's both real and imaginary parts
must match, compatibly with how print() and format()
work for complex numbers.

Failure to create file in tempdir() for compressed
pdf() graphics device no longer errors (then later
segfaults). There is now a warning instead of error and
compression is turned off for the device. Thanks to Alec
Wysoker (PR#17191).

dev.capture() using Quartz Cocoa device (macOS) returned
invalid components if the back-end chose to use ARGB instead of RGBA
image format. (Reported by Noam Ross.)

seq("2", "5") now works too, equivalently to
"2":"5" and seq.int().

seq.int(to = 1, by = 1) is now correct, other cases are
integer (instead of double) when seq() is integer
too, and the "non-finite" error messages are consistent between
seq.default() and seq.int(), no longer mentioning
NaN etc.

rep(x, times) and rep.int(x, times) now work
when times is larger than the largest value representable
in an integer vector. (PR#16932)

download.file(method = "libcurl") does not check for
URL existence before attempting downloads; this is more robust to
servers that do not support HEAD or range-based retrieval, but may
create empty or incomplete files for aborted download requests.

str() no longer shows "list output truncated",
in cases that list was not shown at all. Thanks to Neal Fultz
(PR#17219)

Fix for cairo_pdf() (and svg() and
cairo_ps()) when replaying a saved display list that contains
a mix of grid and graphics output.
(Report by Yihui Xie.)

The str() and as.hclust() methods for
"dendrogram" now also work for deeply nested dendrograms
thanks to non-recursive implementations by Bradley Broom.

sample() now uses two uniforms for added precision
when the uniform generator is Knuth-TAOCP,
Knuth-TAOCP-2002, or a user-defined generator and the
population size is 2^25 or greater.

If a vignette in the ‘vignettes’ directory is listed in
‘.Rbuildignore’, R CMD build would not include it
in the tarball, but would include it in the vignette database,
leading to a check warning. (PR#17246)

Sys.timezone() now returns non-NA also on platforms
such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's
PR#17186.

format(x) for an illegal "POSIXlt" object
x no longer segfaults.

methods(f) now also works for f"("
or "{".

(Windows only) dir.create() did not check the length
of the path to create, and so could overflow a buffer and crash
R. (PR#17206)

On some systems, very small hexadecimal numbers in hex notation
would underflow to zero. (PR#17199)

pmin() and pmax() now work again for
ordered factors and 0-length S3 classed objects, thanks to
Suharto Anggono's PR#17195 and PR#17200.

bug.report() did not do any validity checking on a
package's BugReports field. It now ignores an empty field,
removes leading whitespace and only attempts to open
http:// and https:// URLs, falling back to emailing
the maintainer.

Bandwidth selectors bw.ucv() and
bw.SJ() gave incorrect answers or incorrectly reported an
error (because of integer overflow) for inputs longer than
46341. Similarly for bw.bcv() at length 5793.

Another possible integer overflow is checked and may result in an
error report (rather than an incorrect result) for much longer
inputs (millions for a smooth distribution).

findMethod() failed if the active signature had
expanded beyond what a particular package used. (Example with
packages XR and XRJulia on CRAN.)

qbeta() underflowed too early in some very asymmetric
cases. (PR#17178)

R CMD Rd2pdf had problems with packages with
non-ASCII titles in ‘.Rd’ files (usually the titles were
omitted).

CHANGES IN R 3.3.2

NEW FEATURES

extSoftVersion() now reports the version (if any) of
the readline library in use.

The version of LAPACK included in the sources has been
updated to 3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().

Use options(deparse.max.lines=) to limit the number
of lines recorded in .Traceback and other deparsing
activities.

format(<AsIs>) looks more regular, also for
non-character atomic matrices.

abbreviate() gains an option named = TRUE.

The online documentation for package methods is
extensively rewritten. The goals are to simplify
documentation for basic use, to note old features not
recommended and to correct out-of-date information.

Calls to setMethod() no longer print a message when
creating a generic function in those cases where that is
natural: S3 generics and primitives.

INSTALLATION and INCLUDED SOFTWARE

Versions of the readline library >= 6.3 had been
changed so that terminal window resizes were not signalled to
readline: code has been added using a explicit signal
handler to work around that (when R is compiled against readline
>= 6.3). (PR#16604)

When an S4 class name matches multiple classes in the S4
cache, perform a dynamic search in order to obey namespace
imports. This should eliminate annoying messages about multiple
hits in the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the
cache.

sample(NA_real_) now works.

Packages using non-ASCII encodings in their code did not
install data properly on systems using different encodings.

merge(df1, df2) now also works for data frames with
column names "na.last", "decreasing", or
"method". (PR#17119)

contour() caused a segfault if the labels
argument had length zero. (Reported by Bill Dunlap.)

unique(warnings()) works more correctly, thanks to a
new duplicated.warnings() method.

(Windows only) R CMD SHLIB failed when a symbol
in the resulting library had the same name as a keyword in
the ‘.def’ file. (PR#17130)

pmax() and pmin() now work with (more ?)
classed objects, such as "Matrix" from the Matrix
package, as documented for a long time.

axis(side, x = D) and hence Axis() and
plot() now work correctly for "Date" and time
objects D, even when “time goes backward”, e.g.,
with decreasing xlim. (Reported by William May.)

str(I(matrix(..))) now looks as always intended.

plot.ts(), the plot() method for time series,
now respects cex, lwd and lty. (Reported by
Greg Werbin.)

parallel::mccollect() now returns a named list (as
documented) when called with wait = FALSE. (Reported by
Michel Lang.)

If a package added a class to a class union in another
package, loading the first package gave erroneous warnings
about “undefined subclass”.

c()'s argument use.names is documented now, as
belonging to the (C internal) default method. In
“parallel”, argument recursive is also moved from
the generic to the default method, such that the formal argument list
of base generic c() is just (...).

rbeta(4, NA) and similarly rgamma() and
rnbinom() now return NaN's with a warning, as other
r<dist>(), and as documented. (PR#17155)

Using options(checkPackageLicense = TRUE) no longer
requires acceptance of the licence for non-default standard
packages such as compiler. (Reported by Mikko Korpela.)

split(<very_long>, *) now works even when the split
off parts are long. (PR#17139)

min() and max() now also work correctly when
the argument list starts with character(0). (PR#17160)

Subsetting very large matrices (prod(dim(.)) >= 2^31)
now works thanks to Michael Schubmehl's PR#17158.

bartlett.test() used residual sums of squares
instead of variances, when the argument was a list of lm objects.
(Reported by Jens Ledet Jensen).

plot(<lm>, which = *) now correctly labels the
contour lines for the standardized residuals for which = 6.
It also takes the correct p in case of singularities (also
for which = 5). (PR#17161)

pretty(d, ..) for date-time d rarely failed
when "halfmonth" time steps were tried (PR#16923) and
on ‘inaccurate’ platforms such as 32-bit Windows or
a configuration with --disable-long-double; see comment
#15 of PR#16761.

In text.default(x, y, labels), the rarely(?) used
default for labels is now correct also for the case of a
2-column matrix x and missing y.

as.factor(c(a = 1L)) preserves names() again
as in R < 3.1.0.

strtrim(""[0], 0[0]) now works.

Use of Ctrl-C to terminate a reverse incremental
search started by Ctrl-R in the readline-based Unix
terminal interface is now supported when R was compiled against
readline >= 6.0 (Ctrl-G always worked).
(PR#16603)

CHANGES IN R 3.3.0

SIGNIFICANT USER-VISIBLE CHANGES

nchar(x, *)'s argument keepNA governing how
the result for NAs in x is determined, gets a new
default keepNA = NA which returns NA where
x is NA, except for type = "width" which still
returns 2, the formatting / printing width of NA.

All builds have support for https: URLs in the
default methods for download.file(), url() and code
making use of them.

Unfortunately that cannot guarantee that any particular
https: URL can be accessed. For example, server and client
have to successfully negotiate a cryptographic protocol (TLS/SSL,
...) and the server's identity has to be verifiable via
the available certificates. Different access methods may allow
different protocols or use private certificate bundles: we
encountered a https: CRAN mirror which could be accessed by
one browser but not by another nor by download.file() on
the same Linux machine.

NEW FEATURES

The print method for methods() gains a
byclass argument.

New functions validEnc() and validUTF8() to
give access to the validity checks for inputs used by
grep() and friends.

Also, the names of the R ‘language elements’ are exported
as character vector tools::langElts.

str(x) now displays "Time-Series" also for
matrix (multivariate) time-series, i.e. when is.ts(x) is true.

(Windows only) The GUI menu item to install local packages
now accepts ‘*.tar.gz’ files as well as ‘*.zip’ files
(but defaults to the latter).

New programmeR's utility function chkDots().

D() now signals an error when given invalid input,
rather than silently returning NA. (Request of John Nash.)

formula objects are slightly more “first class”:
e.g., formula() or new("formula", y ~ x) are now
valid. Similarly, for "table", "ordered" and
"summary.table". Packages defining S4 classes with the above
S3/S4 classes as slots should be reinstalled.

New function strrep() for repeating the elements of a
character vector.

news() now displays R and package news files within
the HTML help system if it is available. If no news file is found,
a visible NULL is returned to the console.

as.raster(x) now also accepts raw arrays
x assuming values in 0:255.

Subscripting of matrix/array objects of type
"expression" is now supported.

type.convert("i") now returns a factor instead of a
complex value with zero real part and missing imaginary part.

Graphics devices cairo_pdf() and cairo_ps()
now allow non-default values of the cairographics ‘fallback
resolution’ to be set.

This now defaults to 300 on all platforms: that is the default
documented by cairographics, but apparently was not used by all
system installations.

file() gains an explicit method argument
rather than implicitly using
getOption("url.method", "default").

Thanks to a patch from Tomas Kalibera, x[x != 0] is
now typically faster than x[which(x != 0)] (in the case
where x has no NAs, the two are equivalent).

read.table() now always uses the names for a named
colClasses argument (previously names were only used when
colClasses was too short). (In part, wish of PR#16478.)

(Windows only) download.file() with default
method = "auto" and a ftps:// URL chooses
"libcurl" if that is available.

The out-of-the box Bioconductor mirror has been changed to
one using https://: use chooseBioCmirror() to choose
a http:// mirror if required.

The data frame and formula methods for aggregate()
gain a drop argument.

available.packages() gains a repos argument.

The undocumented switching of methods for url() on
https: and ftps: URLs is confined to
method = "default" (and documented).

smoothScatter() gains a ret.selection argument.

qr() no longer has a ... argument to pass
additional arguments to methods.

[ has a method for class "table".

It is now possible (again) to replayPlot() a
display list snapshot that was created by recordPlot()
in a different R session.

It is still not a good idea to use snapshots as a persistent
storage format for R plots, but it is now not completely silly to
use a snapshot as a format for transferring an R plot between two
R sessions.

tools::undoc(dir = D) and codoc(dir = D) now
also work when D is a directory whose normalizePath()ed
version does not end in the package name, e.g. from a symlink.

abbreviate() has more support for multi-byte
character sets – it no longer removes bytes within characters and
knows about Latin vowels with accents. It is still only
really suitable for (most) European languages, and still warns on
non-ASCII input.

abbreviate(use.classes = FALSE) is now implemented, and
that is more suitable for non-European languages.

match(x, table) is faster (sometimes by an order of
magnitude) when x is of length one and incomparables
is unchanged, thanks to Peter Haverty (PR#16491).

More consistent, partly not back-compatible behavior of
NA and NaN coercion to complex numbers, operations
less often resulting in complex NA (NA_complex_).

lengths() considers methods for length and
[[ on x, so it should work automatically on any
objects for which appropriate methods on those generics are
defined.

The logic for selecting the default screen device on OS X
has been simplified: it is now quartz() if that is
available even if environment variable DISPLAY has been set
by the user.

The choice can easily be overridden via environment
variable R_INTERACTIVE_DEVICE.

recordPlot() has new arguments load and
attach to allow package names to be stored as part of a
recorded plot. replayPlot() has new argument
reloadPkgs to load/attach any package names that were
stored as part of a recorded plot.

S4 dispatch works within calls to .Internal(). This
means explicit S4 generics are no longer needed for
unlist() and as.vector().

Only font family names starting with "Hershey" (and
not "Her" as before) are given special treatment by the
graphics engine.

S4 values are automatically coerced to vector (viaas.vector) when subassigned into atomic vectors.

findInterval() gets a left.open option.

The version of LAPACK included in the sources has been
updated to 3.6.0, including those ‘deprecated’ routines
which were previously included. Ca 40 double-complex
routines have been added at the request of a package maintainer.

As before, the details of what is included are in
‘src/modules/lapack/README’ and this now gives information on
earlier additions.

tapply() has been made considerably more efficient
without changing functionality, thanks to proposals from Peter
Haverty and Suharto Anggono. (PR#16640)

match.arg(arg) (the one-argument case) is faster; so
is sort.int(). (PR#16640)

The format method for object_size objects now
also accepts “binary” units such as "KiB" and e.g.,
"Tb". (Partly from PR#16649.)

Profiling now records calls of the form foo::bar and
some similar cases directly rather than as calls to
<Anonymous>. Contributed by Winston Chang.

New string utilities startsWith(x, prefix) and
endsWith(x, suffix). Also provide speedups for some
grepl("^...",*) uses (related to proposals in PR#16490).

Reference class finalizers run at exit, as well as on
garbage collection.

Avoid parallel dependency on stats for port
choice and random number seeds. (PR#16668)

The radix sort algorithm and implementation from
data.table (forder) replaces the previous radix
(counting) sort and adds a new method for order().
Contributed by Matt Dowle and Arun Srinivasan, the new algorithm
supports logical, integer (even with large values), real, and
character vectors. It outperforms all other methods, but there
are some caveats (see ?sort).

The order() function gains a method argument
for choosing between "shell" and "radix".

New function grouping() returns a permutation that
stably rearranges data so that identical values are adjacent. The
return value includes extra partitioning information on the
groups. The implementation came included with the new radix sort.

rhyper(nn, m, n, k) no longer returns NA when
one of the three parameters exceeds the maximal integer.

switch() now warns when no alternatives are provided.

parallel::detectCores() now has default logical
= TRUE on all platforms – as this was the default on Windows,
this change only affects Sparc Solaris.

Option logical = FALSE is now supported on Linux and recent
versions of OS X (for the latter, thanks to a suggestion of Kyaw
Sint).

hist() for "Date" or "POSIXt" objects
would sometimes give misleading labels on the breaks, as they
were set to the day before the start of the period being
displayed. The display format has been changed, and the shift of the
start day has been made conditional on right = TRUE (the
default). (PR#16679)

R now uses a new version of the logo (donated to the R
Foundation by RStudio). It is defined in ‘.svg’ format, so
will resize without unnecessary degradation when displayed on
HTML pages—there is also a vector PDF version. Thanks to
Dirk Eddelbuettel for producing the corresponding X11 icon.

New function .traceback() returns the stack trace
which traceback() prints.

lengths() dispatches internally.

dotchart() gains a pt.cex argument to control
the size of points separately from the size of plot labels.
Thanks to Michael Friendly and Milan Bouchet-Valat for ideas
and patches.

as.roman(ch) now correctly deals with more diverse
character vectors ch; also arithmetic with the resulting
roman numbers works in more cases. (PR#16779)

prcomp() gains a new option rank. allowing to
directly aim for less than min(n,p) PC's. The
summary() and its print() method have been amended,
notably for this case.

gzcon() gains a new option text, which marks
the connection as text-oriented (so e.g. pushBack()
works). It is still always opened in binary mode.

The import() namespace directive now accepts an
argument except which names symbols to exclude from the
imports. The except expression should evaluate to a
character vector (after substituting symbols for strings). See
Writing R Extensions.

New convenience function Rcmd() in package
tools for invoking R CMD tools from within R.

New functions makevars_user() and
makevars_site() in package tools to determine the
location of the user and site specific ‘Makevars’ files for
customizing package compilation.

UTILITIES

R CMD check has a new option
--ignore-vignettes for use with non-Sweave vignettes
whose VignetteBuilder package is not available.

R CMD check now by default checks code usage
(viacodetools) with only the base package
attached. Functions from default packages other than base
which are used in the package code but not imported are reported
as undefined globals, with a suggested addition to the
NAMESPACE file.

R CMD Rdconv and R CMD Rd2pdf each have
a new option --RdMacros=pkglist which allows Rd macros
to be specified before processing.

DEPRECATED AND DEFUNCT

The previously included versions of zlib,
bzip2, xz and PCRE have been removed, so suitable
external (usually system) versions are required (see the
‘R Installation and Administration’ manual).

The unexported and undocumented Windows-only devices
cairo_bmp(), cairo_png() and cairo_tiff()
have been removed. (These devices should be used as
e.g. bmp(type = "cairo").)

(Windows only) Function setInternet2() has no effect
and will be removed in due course. The choice between methods
"internal" and "wininet" is now made by the
method arguments of url() and download.file()
and their defaults can be set via options. The
out-of-the-box default remains "wininet" (as it has been
since R 3.2.2).

[<- with an S4 value into a list currently embeds the
S4 object into its own list such that the end result is roughly
equivalent to using [[<-. That behavior is deprecated. In
the future, the S4 value will be coerced to a list with
as.list().

Package tools' functions
package.dependencies(), pkgDepends(), etc are
deprecated now, mostly in favor of package_dependencies()
which is both more flexible and efficient.

INSTALLATION and INCLUDED SOFTWARE

Support for very old versions of valgrind
(e.g., 3.3.0) has been removed.

The included libtool script (generated by
configure) has been updated to version 2.4.6 (from 2.2.6a).

libcurl version 7.28.0 or later with support for the
https protocol is required for installation (except on
Windows).

BSD networking is now required (except on Windows) and so
capabilities("http/ftp") is always true.

configure uses pkg-config for PNG, TIFF
and JPEG where this is available. This should work better with
multiple installs and with those using static libraries.

The minimum supported version of OS X is 10.6 (‘Snow
Leopard’): even that has been unsupported by Apple since 2012.

The configure default on OS X is
--disable-R-framework: enable this if you intend to
install under ‘/Library/Frameworks’ and use with R.app.

The minimum preferred version of PCRE has since R 3.0.0
been 8.32 (released in Nov 2012). Versions 8.10 to 8.31 are now
deprecated (with warnings from configure), but will
still be accepted until R 3.4.0.

configure looks for C functions __cospi,
__sinpi and __tanpi and uses these if cospietc are not found. (OS X is the main instance.)

(Windows) R is now built using gcc
4.9.3. This build will require recompilation of at least those packages
that include C++ code, and possibly others. A build of R-devel using
the older toolchain will be temporarily available for comparison
purposes.

During the transition, the environment variable
R_COMPILED_BY has been defined to indicate which toolchain
was used to compile R (and hence, which should be used to compile
code in packages). The COMPILED_BY variable described below
will be a permanent replacement for this.

(Windows) A make and R CMD config variable
named COMPILED_BY has been added. This indicates
which toolchain was used to compile R (and hence, which should be
used to compile code in packages).

PACKAGE INSTALLATION

The make macro AWK which used to be made
available to files such as ‘src/Makefile’ is no longer set.

C-LEVEL FACILITIES

The API call logspace_sum introduced in R 3.2.0 is
now remapped as an entry point to Rf_logspace_sum, and its
first argument has gained a const qualifier. (PR#16470)

Code using it will need to be reinstalled.

Similarly, entry point log1pexp also defined in
‘Rmath.h’ is remapped there to Rf_log1pexp

R_GE_version has been increased to 11.

New API call R_orderVector1, a faster
one-argument version of R_orderVector.

When R headers such as ‘R.h’ and ‘Rmath.h’ are
called from C++ code in packages they include the C++ versions of
system headers such as ‘<cmath>’ rather than the legacy
headers such as ‘<math.h>’. (Headers ‘Rinternals.h’ and
‘Rinterface.h’ already did, and inclusion of system headers
can still be circumvented by defining NO_C_HEADERS,
including as from this version for those two headers.)

The manual has long said that R headers should not be
included within an extern "C" block, and almost all the
packages affected by this change were doing so.

Including header ‘S.h’ from C++ code would fail on some
platforms, and so gives a compilation error on all.

The deprecated header ‘Rdefines.h’ is now compatible
with defining R_NO_REMAP.

The connections interface now includes a function
R_GetConnection() which allows packages implementing
connections to convert R connection objects to
Rconnection handles. Code which previously
used the low-level R-internal getConnection() entry point
should switch.

BUG FIXES

C-level asChar(x) is fixed for when x is not a
vector, and it returns "TRUE"/"FALSE" instead of
"T"/"F" for logical vectors.

The first arguments of .colSums() etc (with an
initial dot) are now named x rather than X (matching
colSums()): thus error messages are corrected.

A coef() method for class "maov" has been
added to allow vcov() to work with multivariate
results. (PR#16380)

Jumps to outer contexts, for example in error recovery, now
make intermediate jumps to contexts where on.exit() actions
are established instead of trying to run all on.exit()
actions before jumping to the final target. This unwinds the stack
gradually, releases resources held on the stack, and significantly
reduces the chance of a segfault when running out of C stack
space. Error handlers established using
withCallingHandlers() and options("error")
specifications are ignored when handling a C stack overflow error
as attempting one of these would trigger a cascade of C stack
overflow errors. (These changes resolve PR#16753.)

The spacing could be wrong when printing a complex array.
(Report and patch by Lukas Stadler.)

pretty(d, n, min.n, *) for date-time objects d
works again in border cases with large min.n, returns a
labels attribute also for small-range dates and in such cases
its returned length is closer to the desired n. (PR#16761)
Additionally, it finally does cover the range of d, as it
always claimed.

tsp(x) <- NULL did not handle correctly objects
inheriting from both "ts" and "mts". (PR#16769)

The data.frame method of rbind() gains an
optional argument stringsAsFactors (instead of only
depending on getOption("stringsAsFactors")).

smooth(x, *) now also works for long vectors.

tools::texi2dvi() has a workaround for problems with
the texi2dvi script supplied by texinfo 6.1.

It extracts more error messages from the LaTeX logs when in
emulation mode.

UTILITIES

R CMD check will leave a log file
‘build_vignettes.log’ from the re-building of vignettes in
the ‘.Rcheck’ directory if there is a problem, and always if
environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is
set to a true value.

DEPRECATED AND DEFUNCT

Use of SUPPORT_OPENMP from header ‘Rconfig.h’ is
deprecated in favour of the standard OpenMP define _OPENMP.

(This has been the recommendation in the manual for a while now.)

The make macro AWK which is long unused by
R itself but recorded in file ‘etc/Makeconf’ is deprecated
and will be removed in R 3.3.0.

The C header file ‘S.h’ is no longer documented: its
use should be replaced by ‘R.h’.

(Windows only) The Rgui front end did not
always initialize the console properly, and could cause
R to crash. (PR#16698)

dummy.coef.lm() now works in more cases, thanks to a
proposal by Werner Stahel (PR#16665). In addition, it now works
for multivariate linear models ("mlm", manova)
thanks to a proposal by Daniel Wollschlaeger.

The as.hclust() method for "dendrogram"s
failed often when there were ties in the heights.

reorder() and midcache.dendrogram() now are
non-recursive and hence applicable to somewhat deeply nested
dendrograms, thanks to a proposal by Suharto Anggono in PR#16424.

cor.test() now calculates very small p values
more accurately (affecting the result only in extreme not
statistically relevant cases). (PR#16704)

smooth(*, do.ends=TRUE) did not always work correctly
in R versions between 3.0.0 and 3.2.3.

pretty(D) for date-time objects D now also
works well if range(D) is (much) smaller than a second. In
the case of only one unique value in D, the pretty range
now is more symmetric around that value than previously.
Similarly, pretty(dt) no longer returns a length 5 vector
with duplicated entries for Date objects dt which
span only a few days.

The figures in help pages such as ?points were
accidentally damaged, and did not appear in R 3.2.3.
(PR#16708)

[dpqr]nbinom(*, size=Inf, mu=.) now works as limit
case, for ‘dpq’ as the Poisson. (PR#16727)pnbinom() no longer loops infinitely in border cases.

approxfun(*, method="constant") and hence ecdf()
which calls the former now correctly “predict” NaN
values as NaN.

summary.data.frame() now displays NAs in
Date columns in all cases. (PR#16709)

CHANGES IN R 3.2.3

NEW FEATURES

Some recently-added Windows time zone names have been added
to the conversion table used to convert these to Olson names.
(Including those relating to changes for Russia in Oct 2014, as in
PR#16503.)

(Windows) Compatibility information has been added to the
manifests for ‘Rgui.exe’, ‘Rterm.exe’ and
‘Rscript.exe’. This should allow win.version() and
Sys.info() to report the actual Windows version up to
Windows 10.

Windows "wininet" FTP first tries EPSV / PASV mode
rather than only using active mode (reported by Dan Tenenbaum).

which.min(x) and which.max(x) may be much
faster for logical and integer x and now also work for long
vectors.

The ‘emulation’ part of tools::texi2dvi() has
been somewhat enhanced, including supporting quiet = TRUE.
It can be selected by texi2dvi = "emulation".

(Windows) MiKTeX removed its texi2dvi.exe command in Sept
2015: tools::texi2dvi() tries texify.exe if it is
not found.

(Windows only) Shortcuts for printing and saving have
been added to menus in Rgui.exe. (Request of PR#16572.)

The included version of PCRE has been updated to 8.38, a
bug-fix release.

View() now displays nested data frames in a more
friendly way. (Request with patch in PR#15915.)

INSTALLATION and INCLUDED SOFTWARE

The included configuration code for libintl has been
updated to that from gettext version 0.19.5.1 — this
should only affect how an external library is detected (and the
only known instance is under OpenBSD). (Wish of PR#16464.)

configure has a new argument
--disable-java to disable the checks for Java.

The configure default for MAIN_LDFLAGS has
been changed for the FreeBSD, NetBSD and Hurd OSes to one more
likely to work with compilers other than gcc (FreeBSD 10
defaults to clang).

CHANGES IN R 3.2.2

SIGNIFICANT USER-VISIBLE CHANGES

It is now easier to use secure downloads from
https:// URLs on builds which support them: no longer do
non-default options need to be selected to do so. In particular,
packages can be installed from repositories which offer
https:// URLs, and those listed by setRepositories()
now do so (for some of their mirrors).

Support for https:// URLs is available on Windows, and on
other platforms if support for libcurl was compiled in and
if that supports the https protocol (system installations
can be expected to do). So https:// support can be
expected except on rather old OSes (an example being OS X
‘Snow Leopard’, where a non-system version of
libcurl can be used).

(Windows only) The default method for accessing URLs viadownload.file() and url() has been changed to be
"wininet" using Windows API calls. This changes the way
proxies need to be set and security settings made: there have been
some reports of ftp: sites being inaccessible under the new default
method (but the previous methods remain available).

NEW FEATURES

cmdscale() gets new option list. for increased
flexibility when a list should be returned.

configure now supports texinfo version 6.0,
which (unlike the change from 4.x to 5.0) is a minor update.
(Wish of PR#16456.)

(Non-Windows only) download.file() with default
method = "auto" now chooses "libcurl" if that is
available and a https:// or ftps:// URL is used.

(Windows only) setInternet2(TRUE) is now the default.
The command-line option --internet2 and environment
variable R_WIN_INTERNET2 are now ignored.

Thus by default the "internal" method for
download.file() and url() uses the "wininet"
method: to revert to the previous default use
setInternet2(FALSE).

This means that https:// URLs can be read by default by
download.file() (they have been readable by file()
and url() since R 3.2.0).

There are implications for how proxies need to be set (see
?download.file).

chooseCRANmirror() and chooseBioCmirror() now
offer HTTPS mirrors in preference to HTTP mirrors. This changes
the interpretation of their ind arguments: see their help
pages.

capture.output() gets optional arguments type
and split to pass to sink(), and hence can be used to
capture messages.

C-LEVEL FACILITIES

Header ‘Rconfig.h’ now defines HAVE_ALLOCA_H if
the platform has the ‘alloca.h’ header (it is needed to
define alloca on Solaris and AIX, at least: see
‘Writing R Extensions’ for how to use it).

INSTALLATION and INCLUDED SOFTWARE

The libtool script generated by
configure has been modified to support FreeBSD >= 10
(PR#16410).

BUG FIXES

The HTML help page links to demo code failed due to a change
in R 3.2.0. (PR#16432)

If the na.action argument was used in
model.frame(), the original data could be
modified. (PR#16436)

getGraphicsEvent() could cause a crash if a graphics
window was closed while it was in use. (PR#16438)

strptime() could overflow the allocated storage on
the C stack when the timezone had a non-standard format much
longer than the standard formats. (Part of PR#16328.)

options(OutDec = s) now signals a warning (which will
become an error in the future) when s is not a string with
exactly one character, as that has been a documented requirement.

prettyNum() gains a new option input.d.mark
which together with other changes, e.g., the default for
decimal.mark, fixes some format()ting variants with
non-default getOption("OutDec") such as in PR#16411.

download.packages() failed for type equal to
either "both" or "binary". (Reported by Dan
Tenenbaum.)

The dendrogram method of labels() is much more
efficient for large dendrograms, now using rapply().
(Comment #15 of PR#15215)

The "port" algorithm of nls() could give
spurious errors. (Reported by Radford Neal.)

Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited
class. Fixing this requires adding the ability for methods to be
“external”, with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses"
in the documentation.

readBin() could fail on the SPARC architecture
due to alignment issues. (Reported by Radford Neal.)

Auto-printing of S3 and S4 values now searches for
print() in the base namespace and show() in the
methods namespace instead of searching the global
environment.

polym() gains a coefs = NULL argument and
returns class "poly" just like poly() which gets a
new simple=FALSE option. They now lead to correct
predict()ions, e.g., on subsets of the original data.
(PR#16239)

ttkimage() did not (and could not) work so was
removed. Ditto for tkimage.cget() and
tkimage.configure(). Added two Ttk widgets and missing
subcommands for Tk's image command:
ttkscale(),
ttkspinbox(),
tkimage.delete(),
tkimage.height(),
tkimage.inuse(),
tkimage.type(),
tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)

getClass("foo") now also returns a class definition when it is
found in the cache more than once.

CHANGES IN R 3.2.1

NEW FEATURES

utf8ToInt() now checks that its input is valid UTF-8
and returns NA if it is not.

install.packages() now allows type = "both"
with repos = NULL if it can infer the type of file.

nchar(x, *) and nzchar(x) gain a new argument
keepNA which governs how the result for NAs in
x is determined. For nzchar() in general and
nchar() in the R 3.2.x series, the default
remains FALSE which is fully back compatible.
From R 3.3.0, nchar()'s default will change to
keepNA = NA and you are advised to consider this for code
portability.

news() more flexibly extracts dates from package
‘NEWS.Rd’ files.

lengths(x) now also works (trivially) for atomic
x and hence can be used more generally as an efficient
replacement of sapply(x, length) and similar.

The included version of PCRE has been updated to 8.37, a
bug-fix release.

diag() no longer duplicates a matrix when extracting
its diagonal.

as.character.srcref() gains an argument to allow
characters corresponding to a range of source references to be
extracted.

BUG FIXES

acf() and ccf() now guarantee values strictly
in [-1,1] (instead of sometimes very slightly outside). PR#15832.

as.integer("111111111111") now gives NA (with a warning) as
it does for the corresponding numeric or negative number
coercions. Further, as.integer(M + 0.1) now gives M
(instead of NA) when M is the maximal representable integer.

On some platforms nchar(x, "c") and nchar(x, "w")
would return values (possibly NA) for inputs which were
declared to be UTF-8 but were not, or for invalid strings without a
marked encoding in a multi-byte locale, rather than give an
error. Additional checks have been added to mitigate this.

plotNode(), the workhorse of the plot method
for "dendrogram"s is no longer recursive, thanks to Suharto
Anggono, and hence also works for deeply nested dendrograms. (PR#15215)

The parser could overflow internally when given numbers
in scientific format with extremely large exponents. (PR#16358)

If the CRAN mirror was not set, install.packages(type = "both")
and related functions could repeatedly query the user for it.
(Part of PR#16362)

The low-level functions .rowSums() etc. did not
check the length of their argument, so could segfault. (PR#16367)

The quietly argument of library() is now
correctly propagated from .getRequiredPackages2().

Under some circumstances using the internal PCRE when
building R from source would cause external libs such as
-llzma to be omitted from the main link.

The .Primitive default methods of the logic operators, i.e.,
!, & and |, now give correct error messages
when appropriate, e.g., for `&`(TRUE) or `!`().
(PR#16385)

cummax(x) now correctly propagates NAs also
when x is of type integer and begins with an NA.

summaryRprof() could fail when the profile contained
only two records. (PR#16395)

HTML vignettes opened using vignette() did not support
links into the rest of the HTML help system. (Links worked properly
when the vignette was opened using browseVignettes() or from
within the help system.)

arima(*, xreg = .) (for d >= 1)
computes estimated variances based on a the number of effective
observations as in R version 3.0.1 and earlier. (PR#16278)

slotNames(.) is now correct for "signature"
objects (mostly used internally in methods).

On some systems, the first string comparison after
a locale change would result in NA.

CHANGES IN R 3.2.0

NEW FEATURES

anyNA() gains a recursive argument.

When x is missing and names is not false
(including the default value), Sys.getenv(x, names) returns
an object of class "Dlist" and hence prints tidily.

(Windows.) shell() no longer consults the
environment variable SHELL: too many systems have been
encountered where it was set incorrectly (usually to a path where
software was compiled, not where it was installed).
R_SHELL, the preferred way to select a non-default shell,
can be used instead.

Some unusual arguments to embedFonts() can now be
specified as character vectors, and the defaults have been changed
accordingly.

(Unix-alikes.) system(cmd, input = ) now uses
‘shell-execution-environment’ redirection, which will be
more natural if cmd is not a single command (but requires a
POSIX-compliant shell). (Wish of PR#15508)

read.fwf() and read.DIF() gain a
fileEncoding argument, for convenience.

Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with
R use a "filepath" attribute.

pmatch() uses hashing in more cases and so is faster
at the expense of using more memory. (PR#15697)

pairs() gains new arguments to select sets of
variables to be plotted against each other.

file.info(, extra_cols = FALSE) allows a minimal set
of columns to be computed on Unix-alikes: on some systems without
properly-configured caching this can be significantly faster with
large file lists.

New function dir.exists() in package base to
test efficiently whether one or more paths exist and are
directories.

dput() and friends gain new controls
hexNumeric and digits17 which output double and
complex quantities as, respectively, binary fractions (exactly,
see sprintf("%a")) and as decimals with up to 17
significant digits.

save(), saveRDS() and serialize() now
support ascii = NA which writes ASCII files using
sprintf("%a") for double/complex quantities. This is
read-compatible with ascii = TRUE but avoids
binary->decimal->binary conversions with potential loss of
precision. Unfortunately the Windows C runtime's lack of C99
compliance means that the format cannot be read correctly there in
R before 3.1.2.

The default for formatC(decimal.mark =) has been
changed to be getOption("OutDec"); this makes it more
consistent with format() and suitable for use in print
methods, e.g. those for classes "density", "ecdf",
"stepfun" and "summary.lm".

getOption("OutDec") is now consulted by the print method
for class "kmeans", by cut(), dendrogram(),
plot.ts() and quantile() when constructing labels
and for the report from legend(trace = TRUE).

printNum() and hence format() and
formatC() give a warning if big.mark and
decimal.mark are set to the same value (period and comma
are not uncommonly used for each, and this is a check that
conventions have not got mixed).

merge() can create a result which uses long vectors
on 64-bit platforms.

dget() gains a new argument keep.source which
defaults to FALSE for speed (dput() and
dget() are most often used for data objects where this can
make dget() many times faster).

Packages may now use a file of common macro definitions in
their help files, and may import definitions from other packages.

A number of macros have been added in the new
‘share/Rd’ directory for use in package overview help pages,
and promptPackage() now makes use of them.

tools::parse_Rd() gains a new permissive
argument which converts unrecognized macros into text. This is
used by utils:::format.bibentry to allow LaTeX markup to be
ignored.

options(OutDec =) can now specify a multi-byte
character, e.g., options(OutDec = "\u00b7") in a UTF-8
locale.

is.recursive(x) is no longer true when x is an
external pointer, a weak reference or byte code; the first enables
all.equal(x, x) when x <- getClass(.).

ls() (aka objects()) and
as.list.environment() gain a new argument sorted.

The "source" attribute (which has not been added to
functions by R since before R version 2.14.0) is no longer
treated as special.

Function returnValue() has been added to give
on.exit() code access to a function's return value for
debugging purposes.

crossprod(x, y) allows more matrix coercions when
x or y are vectors, now equalling
t(x) %*% y in these cases (also reported by Radford Neal).
Similarly, tcrossprod(x,y) and %*% work in more
cases with vector arguments.

The byte-code compiler and interpreter include new
instructions that allow many scalar subsetting and assignment and
scalar arithmetic operations to be handled more efficiently. This
can result in significant performance improvements in scalar
numerical code.

apply(m, 2, identity) is now the same as the matrix
m when it has named row names.

A new function debuggingState() has been added,
allowing to temporarily turn off debugging.

example() gets a new optional argument
run.donttest and tools::Rd2ex() a corresponding
commentDonttest, with a default such that
example(..) in help examples will run \donttest
code only if used interactively (a change in behaviour).

New function extSoftVersion() to report on the
versions of third-party software in use in this session.
Currently reports versions of zlib, bzlib, the
liblzma from xz, PCRE, ICU, TRE and the iconv
implementation.

A similar function grSoftVersion() in package grDevices
reports on third-party graphics software.

Function tcltk::tclVersion() reports the Tcl/Tk version.

Calling callGeneric() without arguments now works
with primitive generics to some extent.

vapply(x, FUN, FUN.VALUE) is more efficient notably
for large length(FUN.VALUE); as extension of PR#16061.

as.table() now allows tables with one or more
dimensions of length 0 (such as as.table(integer())).

names(x) <- NULL now clears the names of call
and ... objects.

library() will report a warning when an insufficient
dependency version is masking a sufficient one later on the
library search path.

A new plot() method for class "raster" has
been added.

New check_packages_in_dir_changes() function in
package tools for conveniently analyzing how changing
sources impacts the check results of their reverse dependencies.

Speed-up from Peter Haverty for ls() and
methods:::.requirePackage() speeding up package loading.
(PR#16133)

New get0() function, combining exists() and
get() in one call, for efficiency.

match.call() gains an envir argument for
specifying the environment from which to retrieve
the ... in the call, if any; this environment was wrong
(or at least undesirable) when the definition argument was
a function.

topenv() has been made .Internal() for
speedup, based on Peter Haverty's proposal in PR#16140.

getOption() no longer calls options() in the main
case.

Optional use of libcurl (version 7.28.0 from Oct 2012
or later) for Internet access:

capabilities("libcurl") reports if this is
available.

libcurlVersion() reports the version in use, and
other details of the "libcurl" build including which URL
schemes it supports.

curlGetHeaders() retrieves the headers for
http://, https://, ftp:// and
ftps:// URLs: analysis of these headers can provide
insights into the ‘existence’ of a URL (it might for example be
permanently redirected) and is so used in R CMD
check --as-cran.

download.file() has a new optional method
"libcurl" which will handle more URL schemes, follow
redirections, and allows simultaneous downloads of multiple
URLs.

url() has a new method "libcurl" which
handles more URL schemes and follows redirections. The default
method is controlled by a new option url.method, which
applies also to the opening of URLs viafile()
(which happens implicitly in functions such as
read.table.)

When file() or url() is invoked with a
https:// or ftps:// URL which the current method
cannot handle, it switches to a suitable method if one is
available.

(Windows.) The DLLs ‘internet.dll’ and
‘internet2.dll’ have been merged. In this version it is safe
to switch (repeatedly) between the internal and Windows internet
functions within an R session.

The Windows internet functions are still selected by flag
--internet2 or setInternet2(). This can be
overridden for an url() connection via its new
method argument.

download.file() has new method "wininet", selected
as the default by --internet2 or setInternet2().

parent.env<- can no longer modify the parent of a
locked namespace or namespace imports environment. Contributed by
Karl Millar.

New function isNamespaceLoaded() for readability and speed.

names(env) now returns all the object names of an
environmentenv, equivalently to
ls(env, all.names = TRUE, sorted = FALSE) and also to
the names of the corresponding list,
names(as.list(env, all.names = TRUE)).
Note that although names() returns a character vector, the
names have no particular ordering.

The memory manager now grows the heap more aggressively. This
reduces the number of garbage collections, in particular while
data or code are loaded, at the expense of slightly increasing the
memory footprint.

New function trimws() for removing leading/trailing
whitespace.

cbind() and rbind() now consider S4 inheritance
during S3 dispatch and also obey deparse.level.

cbind() and rbind() will delegate recursively
to methods::cbind2 (methods::rbind2) when at least
one argument is an S4 object and S3 dispatch fails (due to
ambiguity).

New function hsearch_db() in package utils for
building and retrieving the help search database used by
help.search(), along with functions for inspecting the
concepts and keywords in the help search database.

New function .getNamespaceInfo(), a no-check version
of getNamespaceInfo() mostly for internal speedups.

The help search system now takes \keyword entries in
Rd files which are not standard keywords (as given in
‘KEYWORDS’ in the R documentation directory) as concepts.
For standard keyword entries the corresponding descriptions are
additionally taken as concepts.

New lengths() function for getting the lengths of all
elements in a list.

New function toTitleCase() in package tools,
tailored to package titles.

The matrix methods of cbind() and rbind()
allow matrices as inputs which have 2^31 or more
elements. (For cbind(), wish of PR#16198.)

The default method of image() has an explicit check
for a numeric or logical matrix (which was always required).

URLencode() will not by default encode further URLs
which appear to be already encoded.

BIC(mod) and BIC(mod, mod2) now give non-NA
numbers for arima() fitted models, as nobs(mod) now
gives the number of “used” observations for such models.
This fixes PR#16198, quite differently than proposed there.

The print() methods for "htest",
"pairwise.htest" and "power.htest" objects now have
a digits argument defaulting to (a function of)
getOption("digits"), and influencing all printed numbers
coherently. Unavoidably, this changes the display of such test
results in some cases.

Code completion for namespaces now recognizes all loaded
namespaces, rather than only the ones that are also attached.

The code completion mechanism can now be replaced by a
user-specified completer function, for (temporary) situations
where the usual code completion is inappropriate.

unzip() will now warn if it is able to detect truncation
when unpacking a file of 4GB or more (related to PR#16243).

methods() reports S4 in addition to S3 methods;
output is simplified when the class argument is
used. .S3methods() and methods::.S4methods() report
S3 and S4 methods separately.

Higher order functions such as the apply functions
and Reduce() now force arguments to the functions they apply
in order to eliminate undesirable interactions between lazy
evaluation and variable capture in closures. This resolves
PR#16093.

INSTALLATION and INCLUDED SOFTWARE

The \donttest sections of R's help files can be
tested bymake check TEST_DONTTEST=TRUE .

It is possible to request the use of system
valgrind headers viaconfigure option
--with-system-valgrind-headers: note the possible future
incompatibility of such headers discussed in the 'R Installation
and Administration' manual. (Wish of PR#16068.)

The included version of liblzma has been updated to
xz-utils 5.0.7 (minor bug fixes from 5.0.5).

configure options --with-system-zlib,
--with-system-bzlib and --with-system-pcre are
now the default. For the time being there is fallback to the
versions included in the R sources if no system versions are
found or (unlikely) if they are too old.

Linux users should check that the -devel or -dev
versions of packages zlib, bzip2/libbz2 and
pcre as well as xz-devel/liblzma-dev (or
similar names) are installed.

configure by default looks for the
texi2any script from texinfo 5.1 or later, rather
than the makeinfo program. (makeinfo is a
link to the Perl script texi2any in texinfo 5.x.)

The HTML generated by tools::Rd2HTML() and
tools::toHTML() methods is now
‘XHTML 1.0 Strict’.

The compiler package's utility function
setCompilerOptions() now returns the old values
invisibly. The initial optimization level can also be set with the
environment variable R_COMPILER_OPTIMIZE.

R CMD build adds a NeedsCompilation field
if one is not already present in the ‘DESCRIPTION’ file.

R CMD check gains option --test-dir to
specify an alternative set of tests to run.

R CMD check will now by default continue with
testing after many types of errors, and will output a summary
count of errors at the end if any have occurred.

R CMD check now checks that the Title and
Description fields are correctly terminated.

R CMD check --as-cran now:

checks a ‘README.md’ file can be processed: this
needs pandoc installed.

checks the existence and accessibility of URLs in the
‘DESCRIPTION’, ‘CITATION’, ‘NEWS.Rd’ and
‘README.md’ files and in the help files (provided the build
has libcurl support).

reports non-ASCII characters in R source files when there
is no package encoding declared in the ‘DESCRIPTION’ file.

reports (apparent) S3 methods exported but not registered.

reports overwriting registered S3 methods from
base/recommended packages. (Such methods are replaced in the
affected package for the rest of the session, even if the
replacing namespace is unloaded.)

reports if the Title field does not appear to be in
title case (see ‘Writing R Extensions’: there may be
false positives, but note that technical words should be
single-quoted and will then be accepted).

Most of these checks can also be selected by environment
variables: see the ‘R Internals’ manual.

C-LEVEL FACILITIES

New C API utility logspace_sum(logx[], n).

Entry points rbinom_mu, rnbinom_mu and
rmultinom are remapped (by default) to Rf_rbinom_mu
etc. This requires packages using them to be re-installed.

.C(DUP = FALSE) and .Fortran(DUP = FALSE) are
now ignored, so arguments are duplicated if DUP = TRUE
would do so. As their help has long said, .Call() is much
preferred.

New entry point R_allocLD, like R_alloc but
guaranteed to have sufficient alignment for long double
pointers.

isPairList() now returns TRUE for DOTSXP.

WINDOWS BUILD CHANGES

A number of changes to the Windows build system are in development.
The following are currently in place.

Installation using external binary distributions
of zlib, bzip2, liblzma, pcre,
libpng, jpeglib and libtiff is now required,
and the build instructions have been revised.

A new make target rsync-extsoft has been
added to obtain copies of the external libraries from
CRAN.

Building the manuals now requires texi2any from
texinfo 5.1 or later. CRAN binary builds include
the manuals, but by default builds from source will not, and they
will be accessed from CRAN. See the comments in
‘src/gnuwin32/MkRules.dist’ for how to specify the location
of texi2any.

(Windows) Changes have been made to support an experimental
Windows toolchain based on GCC 4.9.2. The default toolchain
continues to be based on GCC 4.6.3, as the new toolchain is not
yet stable enough. A change to a new toolchain is expected during
the R 3.2.x lifetime.

PACKAGE INSTALLATION

(Windows) The use of macro ZLIB_LIBS in file
‘src/Makevars.win’ (which has not been documented for a long
time) now requires an external ‘libz.a’ to be available (it is
part of the ‘goodies’ used to compile Windows binary
packages). It would be simpler to use -lz instead.

The default for option pkgType on platforms using
binary packages is now "both", so source packages will be
tried if binary versions are not available or not up to date.

There are options for what install.packages(type = "both")
(possibly called viaupdate.packages()) will do if
compilation of a source package is desirable: see ?options
(under utils).

If you intend not to accept updates as source packages, you should
use update.packages(type = "binary").

DEPRECATED AND DEFUNCT

download.file(method = "lynx") is defunct.

Building R using the included versions of zlib,
bzip2, xz and PCRE is deprecated: these are frozen
(bar essential bug-fixes) and will be removed for R 3.3.0.

The configure option
--with-valgrind-instrumentation=3 has been withdrawn, as
it did not work with recent valgrind headers: it is now
treated as level 2.

The MethodsList class in package methods had
been deprecated in R 2.11.0 and is defunct now. Functions using
it are defunct if they had been deprecated in R 2.11.0, and are
deprecated now, otherwise.

BUG FIXES

Fixed two obscure bugs in pairlist subassignment, reported by
Radford Neal as part of pqR issue 16.

Fixes for bugs in handling empty arguments and argument
matching by name in log().

eigen(m) now defaults to symmetric = TRUE even
when the dimnames are asymmetric if the matrix is otherwise
symmetric. (PR#16151)

Fix issues with forwarding ... through
callGeneric() and callNextMethod(). (PR#16141)

callGeneric() now works after a callNextMethod().

Subclass information is kept consistent when replacing an
ordinary S4 class with an “old class” via the
S4Class argument to setOldClass(). Thus, for
example, a data.frame is valid for a list argument
in the signature, and a factor is valid for vector
arguments.

In qbeta() the inversion of pbeta() is much
more sophisticated. This works better in corner cases some of
which failed completely previously (PR#15755), or were using
too many iterations.

Auto-printing no longer duplicates objects when printing is
dispatched to a method.

capabilities() has a new item long.double
which indicates if the build uses a long double type which
is longer than double.

nlm() no longer modifies the callback argument in
place (a new vector is allocated for each invocation, which mimics
the implicit duplication that occurred in R < 3.1.0); note that
this is a change from the previously documented
behavior. (PR#15958)

HTML conversion of \href markup in ‘.Rd’ files
did not remove the backslash from \% and so gave an
invalid URL. In a related change, the \ escape is now
required in such URLs.

CHANGES IN R 3.1.2

NEW FEATURES

embedFonts() now defaults to
format = "ps2write" for ‘.ps’ and ‘.eps’ files.
This is available in Ghostscript 9.x (since 2010) whereas the
previous default, format = "pswrite", was removed in
Ghostscript 9.10.

For consistency with [dpqr]norm(),
[dp]lnorm(sdlog = 0) model a point mass at
exp(mulog) rather than return NaN (for an error).

capabilities() now reports if ICU is compiled in for
use for collation (it is only actually used if a suitable locale
is set for collation, and never for a C locale).

(OS X only.) Package tcltk checks when loaded if it is
linked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
component and the X11 libraries are installed. This allows more
informative error messages to be given advising the installation
of the missing component or of XQuartz.

The X11() device and X11-based versions of the data editor
and viewer (invoked by edit() and View() for data
frames and matrices from command-line R) check that the X11
libraries are installed and if not advises installing XQuartz.

icuSetCollate() allows locale = "default", and
locale = "none" to use OS services rather than ICU for
collation.

Environment variable R_ICU_LOCALE can be used to set the
default ICU locale, in case the one derived from the OS locale is
inappropriate (this is currently necessary on Windows).

New function icuGetCollate() to report on the ICU
collation locale in use (if any).

The Bioconductor ‘version’ used by
setRepositories() now defaults to 3.0. (It can be
set at runtime via environment variable
R_BIOC_VERSION.)

Omegahat is no longer listed as providing Windows binary
packages, e.g. by setRepositories(). It has no binary
packages available for R 3.1.x and those for earlier versions
were 32-bit only.

INSTALLATION and INCLUDED SOFTWARE

The configure script reports on the more important
capabilities/options which will not be compiled in.

More types of external BLAS are recognized by name in that report.

When building R as a shared library, the
-L${R_HOME}/lib${R_ARCH} flag is placed earlier in the
link commands used during installation and when packages are
installed: this helps ensure that the current build has priority
if an R shared library has already been installed by
e.g. install-libR in a library mentioned in
LDFLAGS (and not in ‘your system's library directory’
as documented). (Wish of PR#15790.)

LaTeX package upquote is no longer required for R's
use of inconsolata.

(Windows only) If both 32- and 64-bit versions of R are
installed, the ‘bin/R.exe’ and ‘bin/Rscript.exe’ executables
now run 64-bit R. (To run 32-bit R, overwrite these files
with copies of ‘bin/i386/Rfe.exe’.)

UTILITIES

Running R CMD check with
_R_CHECK_DEPENDS_ONLY_ true now makes the
VignetteBuilder packages available even if they are
listed in Suggests, since they are needed to recognise and
process non-Sweave vignettes.

R CMD check now reports empty importFrom
declarations in a ‘NAMESPACE’ file, as these are common
errors (writing importFrom(Pkg) where
import(Pkg) was intended).

R CMD check now by default checks code usage
directly on the package namespace without loading and attaching
the package and its suggests and enhances. For good practice with
packages in the Suggests field, see §1.1.3.1 of
‘Writing R Extensions’. For use of lazy-data objects in
the package's own code, see ?data.

BUG FIXES

dmultinom() did not handle non-finite probabilities
correctly.

prettyNum(x, zero.print=*) now also works when
x contains NAs.

A longstanding bug exhibited by nlminb() on Windows
was traced to a compiler bug in gcc 4.6.3; a workaround has been
put in place. (PR#15244 and PR#15914).

Rendering of \command in HTML versions of help pages
has been improved: this is particularly evident on the help page
for INSTALL.

as.hexmode(x) and as.octmode(x) now behave
correctly for some numeric x, e.g., c(NA, 1) or
c(1, pi).

drop1() failed if the scope argument had
no variables to drop. (PR#15935)

edit() (and hence fix()) failed if
an object had a non-character attribute named "source"
(an attribute that had been used in R prior to version 2.14.0).

callGeneric() could fail if the generic had
... as a formal argument. (PR#15937).

Forking in package parallel called C entry point
exit in the child. This was unsafe (_exit should
have been called), and could flush stdin of the main R
process (seen most often on Solaris).

As good practice, stdout is now flushed before forking a child.

R objects such as list(`a\b` = 1) now print correctly.

getAnywhere("C_pbinom") now returns correctly a
single object (rather than unlisting it).

The confint() method for nls() fits failed it
these has specified parameter limits despite using an algorithm
other than "port". (PR#15960)

Subclassing an S4 class failed if the class required
arguments to the generator, through its initialize() method.

removeSource() did not properly handle expressions
containing arguments that were supplied as missing, e.g.
x[i,]. (PR#15957)

as.environment(list()) now works, and
as.list() of such an environment is now the same as
list(). (PR#15926)

Several tcltk functions failed when run in unusual
environments. (PR#15970)

merge(<dendrogram>, ..) now works correctly for two
‘independent’ dendrograms (PR#15648), and still compatibly
viaadjust = "auto" e.g. for two branches of an
existing dendrogram.

The plot method for "hclust" objects gets an
optional argument check; when that is true (the default) it
checks more carefully for valid input.

(Windows only) If a user chose to install 64 bit R but not
32 bit R, the ‘bin/R’ and ‘bin/Rscript’ executables
failed to run. (PR#15981)

Various possible buffer overruns have been prevented,
and missed memory protection added. (PR#15990)

Rscript no longer passes --args to
R when there are no extra (“user”) arguments.

objects like getClass("refClass")@prototype now
print() and str() without error.

identical() now also looks at the S4 bit.

hist(x, breaks) is more robust in adding a small fuzz
to few breaks when some are very large. (PR#15988)

sub() and gsub() did not handle regular
expressions like "\s{2,}" properly if the text
contained NA or non-ASCII elements in a UTF-8
locale. Part of this was due to a bug in the TRE library.
(PR#16009)

RShowDoc("NEWS") now displays the PDF version.

Matrices and arrays with last dimension zero did not print
at all or incompletely. (PR#16012)

bw.SJ(x) and other bw.*() no longer segfault when
x contains non-finite values. (PR#16024)

R CMD Rd2pdf unintentionally ignored its
--os option.

The internal method of download.file() was not
reporting file sizes and progress correctly on files larger than
2GB (inherited from libxml2). This is corrected for 64-bit
builds (32-bit platforms may not support such files, but where
possible will be supported in future versions of R).

Work around a bug in OS X Yosemite where key environment
variables may be duplicated causing issues in subprocesses. The
duplicates are now removed on R startup (via
Rprofile). (PR#16042)

CHANGES IN R 3.1.1

NEW FEATURES

When attach() reports conflicts, it does so
compatibly with library() by using message().

R CMD Sweave no longer cleans any files by
default, compatibly with versions of R prior to 3.1.0. There are
new options --clean, --clean=default and
--clean=keepOuts.

tools::buildVignette() and tools::buildVignettes()
with clean = FALSE no longer remove any created files.
buildvignette() gains a keep argument for more
cleaning customization.

The Bioconductor ‘version’ used by
setRepositories() can now be set by environment variable
R_BIOC_VERSION at runtime, not just when R is installed.
(It has been stated that Bioconductor will switch from
‘version’ 2.14 to ‘version’ 3.0 during the lifetime
of the R 3.1 series.)

Error messages from bugs in embedded Sexpr code
in Sweave documents now report the source location.

type.convert(), read.table() and similar
read.*() functions get a new numerals argument,
specifying how numeric input is converted when its conversion to
double precision loses accuracy. The default value,
"allow.loss" allows accuracy loss, as in R versions before
3.1.0.

For some compilers, integer addition could overflow without
a warning. R's internal code for both integer addition and
subtraction is more robust now. (PR#15774)

The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().

dbeta(, a,b), pbeta(), qbeta() and
rbeta() are now defined also for a = 0, b = 0,
or infinite a and b (where they typically returned
NaN before).

Many package authors report that the RStudio graphics device
does not work correctly with their package's use of
dev.new(). The new option dev.new(noRStudioGD =
TRUE) replaces the RStudio override by the default device as
selected by R itself, still respecting environment variables
R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE.

readRDS() now returns visibly.

Modifying internal logical scalar constants now results in
an error instead of a warning.

install.packages(repos = NULL) now accepts
http:// or ftp:// URLs of package archives as well
as file paths, and will download as required. In most cases
repos = NULL can be deduced from the extension of the URL.

The warning when using partial matching with the $
operator on data frames is now only given when
options("warnPartialMatchDollar") is TRUE.

Package help requests like package?foo now
try the package foo whether loaded or not.

General help requests now default to trying all loaded
packages, not just those on the search path.

Added a new function promptImport(), to generate a
help page for a function that was imported from another package
(and presumably re-exported, or help would not be needed).

INSTALLATION and INCLUDED SOFTWARE

configure option --with-internal-tzcode
can now be used with variable rsharedir.

The included version of PCRE has been updated to 8.35.

There is a new target make uninstall-libR to
remove an installed shared/static ‘libR’.

make install-libR now works if a sub-architecture is
used, although the user will need to specify libdir
differently for different sub-architectures.

There is more extensive advice on which LaTeX packages are
required to install R or to make package manuals (as done by
R CMD check) in the ‘Writing R Extensions’
manual.

Compilers/linkers were handling the visibility control in
‘src/extra/xz’ inconsistently (and apparently in some cases
incorrectly), so it has been simplified. (PR#15327)

(Windows) There is updated support for the use of ICU for
collation: see the ‘R Installation and Administration Manual’.

BUG FIXES

dbinom(x, n), pbinom(), dpois(), etc,
are slightly less restrictive in checking if n is
integer-valued. (Wish of PR#15734.)

The "CRAN" filter (see available.packages())
no longer removes duplicates other than of packages on CRAN, and
does not fail if there is no CRAN repository in
getOption("repos").

The device listing from dev2bitmap() and
bitmap() was truncated to 1000 characters: modern versions
of GhostScript on most platforms have many more devices.

(Windows.) Commands such as Sys.which() and
pipe() which needed to find the full path to a command
could segfault if the ‘long’ path name was much longer than
the ‘short’ path name (which Sys.which() returns),
as the behaviour of the Windows API call had changed.

R CMD build will fail with an error if one of the
packages specified in the VignetteBuilder field is not
installed. (Without loading those packages it cannot be
ascertained which files are intended to be vignettes. This means
that the VignetteBuilder packages have to be installed for
package checking too.)
(Wish of PR#15775.)

Misguided attempts to use chull() with non-finite
points now give an error (related to PR#15777).

For a formula with exactly 32 variables the 32nd variable
was aliased to the intercept in some C-level computations of
terms, so that for example attempting to remove it would remove
the intercept instead (and leave a corrupt internal structure).
(PR#15735)

anyDuplicated() silently returned wrong values when
the first duplicate was at an index which was too large to be
stored in an integer vector (although a lot of RAM and patience
would have been needed to encounter this).

tools::Rd2ex(commentDontrun = FALSE) failed if the
block had only one line.

Hexadecimal constants such as 0x110p-5L which were
incorrectly qualified by L were parsed incorrectly since R
3.0.0, with a slightly garbled warning. (PR#15753)

system() returned success on some platforms even if
the system was unable to launch a process. (PR#15796)

(Windows Rgui console.) Unbuffered output was
sometimes not output immediately if the prompt was not on the last
line of the console.

The built-in help server did not declare the encoding for
the ‘DESCRIPTION’ or other text files to be the package
encoding, so non-ASCII characters could be displayed incorrectly.

R is now trying harder to not cleanup child processes
that were not spawned by mcparallel() on platforms that
provide information about the source process of the SIGCHLD
signal. This allows 3rd party libraries to manage the exit status
of children that they spawn without R interfering.

mcmapply() was only parallelizing if the number of
jobs was bigger than the number of cores. It now parallelizes if
the number of jobs is more than one.

Auto-printing would re-evaluate its argument when trying to
dispatch to a print method. This is now avoided when possible.

Unserializing (including load() and readRDS())
could silently return incorrect numeric values from ASCII saves if
there was a read error.

getParseData() could return incorrect values for
the parents of some elements. (Reported by Andrew Redd.)

Attempting to use data frames of 2^31 or more rows with
merge() or to create a merged data frame of that size now
gives a clearer error message.

parse() did not check its file argument was a
connection if it was not a character string, so
e.g. parse(FALSE) attempted to read from stdin.

Nor did dump() and dput().

The "help.try.all.packages" option was ignored when
the shortcut syntax for help was used, e.g. ?foo.

A potential segfault in string allocation has been fixed.
(Found by Radford Neal.)

Potential memory protection errors in sort() and
D() have been fixed. (Found by Radford Neal.)

Fixed a lack of error checking in graphics event functions.
(Found by Radford Neal; a different patch used here than the
one in pqR.)

The "table" method for as.data.frame() (also
useful as as.data.frame.table()) now passes sep and
base arguments to provideDimnames().

uniroot() gets new optional arguments, notably
extendInt, allowing to auto-extend the search interval when
needed. The return value has an extra component, init.it.

switch(f, ...) now warns when f is a factor,
as this typically happens accidentally where the useR meant to
pass a character string, but f is treated as integer (as
always documented).

The parser has been modified to use less memory.

The way the unary operators (+ - !) handle attributes
is now more consistent. If there is no coercion, all attributes
(including class) are copied from the input to the result:
otherwise only names, dims and dimnames are.

colorRamp() and colorRampPalette() now allow
non-opaque colours and a ramp in opacity via the new argument
alpha = TRUE. (Suggested by Alberto Krone-Martins, but
optionally as there are existing uses which expect only RGB values.)

grid.show.layout() and grid.show.viewport()
get an optional vp.ex argument.

There is a new function find_gs_cmd() in the
tools package to locate a GhostScript executable. (This is
an enhanced version of a previously internal function there.)

object.size() gains a format() method.

There is a new family, "ArialMT", for the
pdf() and postscript() devices. This will only be
rendered correctly on viewers which have access to Monotype
TrueType fonts (which are sometimes requested by journals).

The text and PDF news files, including ‘NEWS’ and
‘NEWS.2’, have been moved to the ‘doc’ directory.

New functions cospi(x), sinpi(x), and
tanpi(x), for more accurate computation of
cos(pi*x), etc, both in R and the C API. Using these
gains accuracy in some cases, e.g., inside lgamma() or
besselI(). (Suggested by Morten Welinder in PR#15529.)

print.table(x, zero.print = ".") now also has an
effect when x is not integer-valued.

There is more support to explore the system's idea of
time-zone names. Sys.timezone() tries to give the current
system setting by name (and succeeds at least on Linux, OS X,
Solaris and Windows), and OlsonNames() lists the names in
the system's Olson database. Sys.timezone(location = FALSE)
gives the previous behaviour.

Platforms with a 64-bit time_t type are allowed to
handle conversions between the "POSIXct" and
"POSIXlt" classes for date-times outside the 32-bit range
(before 1902 or after 2037): the existing workarounds are used on
other platforms. (Note that time-zone information for post-2037
is speculative at best, and the OS services are tested for known
errors and so not used on OS X.)

Currently time_t is usually long and hence 64-bit on
Unix-alike 64-bit platforms: however in several cases the
time-zone database is 32-bit. For R for Windows it is 64-bit
(for both architectures as from this version).

The "save.defaults" option can include a value for
compression_level. (Wish of PR#15579.)

colSums() and friends now have support for arrays and
data-frame columns with 2^31 or more elements.

as.factor() is faster when f is an unclassed
integer vector (for example, when called from tapply()).

fft() now works with longer inputs, from the 12
million previously supported up to 2 billion. (PR#15593)

Complex svd() now uses LAPACK subroutine
ZGESDD, the complex analogue of the routine used for the
real case.

Sweave now outputs ‘.tex’ files in UTF-8 if the
input encoding is declared to be UTF-8, regardless of the
local encoding. The UTF-8 encoding may now be declared using
a LaTeX comment containing the string %\SweaveUTF8
on a line by itself.

file.copy() gains a copy.date argument.

Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for Paris
pre-1940 this could be LMT, PMT, WET or
WEST. To enable this, the "POSIXlt" class has an
optional component "zone" recording the abbreviation for
each element.

For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.

(On Windows, by default on OS X and optionally elsewhere.)
The system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.

read.table(), readLines() and scan()
have a new argument to influence the treatment of embedded nuls.

Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and
ans[[i]] <- tmp: some package code has relied on there
being copies.

Also, a number of other changes to reduce copying of objects; all
contributed by or based on suggestions by Michael Lawrence.

The fast argument of KalmanLike(),
KalmanRun() and KalmanForecast() has been replaced
by update, which instead of updating mod in place,
optionally returns the updated model in an attribute "mod"
of the return value.

arima() and makeARIMA() get a new optional
argument SSinit, allowing the choice of a different
state space initialization which has been observed
to be more reliable close to non-stationarity: see PR#14682.

warning() has a new argument noBreaks., to
simplify post-processing of output with options(warn = 1).

pushBack() gains an argument encoding, to
support reading of UTF-8 characters using scan(),
read.table() and related functions in a non-UTF-8 locale.

all.equal.list() gets a new argument use.names
which by default labels differing components by names (if they
match) rather than by integer index. Saved R output in packages may
need to be updated.

The methods for all.equal() and
attr.all.equal() now have argument check.attributes
after ... so it cannot be partially nor positionally
matched (as it has been, unintentionally).

A side effect is that some previously undetected errors of passing
empty arguments (no object between commas) to all.equal()
are detected and reported.

There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or
numeric. This catches some unintended positional matching.

The message for all.equal.numeric() reports a
"scaled difference" only for scale != 1.

file.path() removes any trailing separator on
Windows, where they are invalid (although sometimes accepted).
This is intended to enhance the portability of code written by
those using POSIX file systems (where a trailing / can be
used to confine path matching to directories).

Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.

mcparallel() gains an option detach = TRUE
which allows execution of code independently of the current
session. It is based on a new estranged = TRUE argument to
mcfork() which forks child processes such that they become
independent of the parent process.

The pdf() device omits circles and text at extremely
small sizes, since some viewers were failing on such files.

The rightmost break for the "months",
"quarters" and "years" cases of
hist.POSIXlt() has been increased by a day. (Inter alia,
fixes PR#15717.)

The handling of DF[i,] <- a where i is of
length 0 is improved. (Inter alia, fixes PR#15718.)

hclust() gains a new method "ward.D2" which
implements Ward's method correctly. The previous "ward"
method is "ward.D" now, with the old name still working.
Thanks to research and proposals by Pierre Legendre.

The sunspot.month dataset has been amended and
updated from the official source, whereas the sunspots and
sunspot.year datasets will remain immutable. The
documentation and source links have been updated correspondingly.

The summary() method for "lm" fits warns if
the fit is essentially perfect, as most of the summary may be
computed inaccurately (and with platform-dependent values).

Programmers who use summary() in order to extract just
a component which will be reliable (e.g., $cov.unscaled)
should wrap their calls in suppressWarnings().

INSTALLATION and INCLUDED SOFTWARE

The included version of LAPACK has been updated to 3.5.0.

There is some support for parallel testing of an
installation, by setting TEST_MC_CORES to an integer
greater than one to indicate the maximum number of cores to be
used in parallel. (It is worth specifying at least 8 cores if
available.) Most of these require a make program (such
as GNU make and dmake) which supports the
$MAKE -j nproc syntax.

Except on Windows: the tests of standard package examples in
make check are done in parallel. This also applies to
running tools::testInstalledPackages().

The more time-consuming regression tests are done in parallel.

The package checks in make check-devel and make
check-recommended are done in parallel.

More of make check will work if recommended packages
are not installed: but recommended packages remain needed for
thorough checking of an R build.

The version of tzcode included in
‘src/extra/tzone’ has been updated. (Formerly used only on
Windows.)

The included (64-bit) time-zone conversion code and Olson
time-zone database can be used instead of the system version: use
configure option --with-internal-tzcode. This
is the default on Windows and OS X. (Note that this does not
currently work if a non-default rsharedirconfigure variable is used.)

(It might be necessary to set environment variable TZ on
OSes where this is not already set, although the system timezone is
deduced correctly on at least Linux, OS X and Windows.)

This option also switches to the version of strftime
included in directory ‘src/extra/tzone’.

configure now tests for a C++11-compliant compiler
by testing some basic features. This by default tries flags for
the compiler specified by CXX, but an alternative compiler,
options and standard can be specified by variables CXX1X,
CXX1XFLAGS and CXX1XSTD (e.g., -std=gnu++11).

R can now optionally be compiled to use reference
counting instead of the NAMED mechanism by defining
SWITCH_TO_REFCNT in ‘Rinternals.h’. This may become
the default in the future.

There is a new option --use-system-tre to use a
suitable system tre library: at present this means a version
from their git repository, after corrections.
(Wish of PR#15660.)

PACKAGE INSTALLATION

The CRANextra repository is no longer a default
repository on Windows: all the binary versions of packages from
CRAN are now on CRAN, although CRANextra contains packages
from Omegahat and elsewhere used by CRAN packages.

Only vignettes sources in directory ‘vignettes’ are
considered to be vignettes and hence indexed as such.

In the ‘DESCRIPTION’ file,

License: X11

is no longer recognized as valid. Use MIT or
BSD_2_clause instead, both of which need + file LICENSE.

For consistency, entries in ‘.Rinstignore’ are now matched
case-insensitively on all platforms.

Help for S4 methods with very long signatures now tries
harder to split the description in the Usage field to no
more than 80 characters per line (some packages had over 120
characters).

There is support for compiling C++11 code in packages on
suitable platforms: see ‘Writing R Extensions’.

Fake installs now install the contents of directory
‘inst’: some packages use this to install e.g. C++ headers
for use by other packages that are independent of the package
itself. Option --no-inst can be used to get the previous
behaviour.

DEBUGGING

The behaviour of the code browser has been made more
consistent, in part following the suggestions in PR#14985.

Calls to browser() are now consistent with calls
to the browser triggered by debug(), in that Enter
will default to n rather than c.

A new browser command s has been added, to
“step into” function calls.

A new browser command f has been added, to
“finish” the current loop or function.

Within the browser, the command help will
display a short list of available commands.

UTILITIES

Only vignettes sources in directory ‘vignettes’ are
considered to be vignettes by R CMD check. That has
been the preferred location since R 2.14.0 and is now obligatory.

For consistency, R CMD build now matches entries
in ‘.Rbuildignore’ and ‘vignettes/.install_extras’
case-insensitively on all platforms (not just on Windows).

checkFF() (called by R CMD check by
default) can optionally check foreign function calls for
consistency with the registered type and argument count. This is
the default for R CMD check --as-cran or can be enabled
by setting environment variable _R_CHECK_FF_CALLS_ to
registration (but is in any case suppressed by
--install=no). Because this checks calls in which
.NAME is an R object and not just a literal character
string, some other problems are detected for such calls.

Functions suppressForeignCheck() and dontCheck()
have been added to allow package authors to suppress false
positive reports.

R CMD check --as-cran warns about a false value of
the ‘DESCRIPTION’ field BuildVignettes for Open Source
packages, and ignores it. (An Open Source package needs to have
complete sources for its vignettes which should be usable on a
suitably well-equipped system).

R CMD Sweave and R CMD Stangle now
process both Sweave and non-Sweave vignettes. The
tools::buildVignette() function has been added to do the
same tasks from within R.

The flags returned by R CMD config --ldflags and
(where installed) pkg-config --libs libR are now those
needed to link a front-end against the (shared or static) R
library.

‘Sweave.sty’ has a new option [inconsolata].

R CMD check customizations such as
_R_CHECK_DEPENDS_ONLY_ make available packages only in
LinkingTo only for installation, and not for
loading/runtime tests.

tools::checkFF() reports on .C and
.Fortran calls with DUP = FALSE if argument
check_DUP is true. This is selected by
R CMD check by default.

R CMD check --use-gct can be tuned to
garbage-collect less frequently using gctorture2()via the setting of environment variable
_R_CHECK_GCT_N_.

Where supported, tools::texi2dvi() limits the number
of passes tried to 20.

C-LEVEL FACILITIES

(Windows only) A function R_WaitEvent() has been
added (with declaration in header‘R.h’) to block execution
until the next event is received by R.

Remapping in the ‘Rmath.h’ header can be suppressed by
defining R_NO_REMAP_RMATH.

The remapping of rround() in header ‘Rmath.h’
has been removed: use fround() instead.

ftrunc() in header ‘Rmath.h’ is now a wrapper
for the C99 function trunc(), which might as well be used
in C code: ftrunc() is still needed for portable C++ code.

The never-documented remapping of prec() to
fprec() in header ‘Rmath.h’ has been removed.

The included LAPACK subset now contains ZGESDD and
ZGELSD.

The function LENGTH() now checks that it is only
applied to vector arguments. However, in packages length()
should be used. (In R itself LENGTH() is a macro without
the function overhead of length().)

Calls to SET_VECTOR_ELT() and SET_STRING_ELT()
are now checked for indices which are in-range: several packages
were writing one element beyond the allocated length.

allocVector3 has been added which allows custom
allocators to be used for individual vector allocations.

DEPRECATED AND DEFUNCT

chol(pivot = TRUE, LINPACK = TRUE) is defunct.

Arguments EISPACK for eigen() and LINPACK for
chol(), chol2inv(), solve() and svd()
are ignored: LAPACK is always used.

.find.package() and .path.package() are
defunct: only the versions without the initial dot introduced in
R 2.13.0 have ever been in the API.

Partial matching when using the $ operator on
data frames now throws a warning and may become defunct in the
future. If partial matching is intended, replace foo$bar
by foo[["bar", exact = FALSE]].

The long-deprecated use of \synopsis in the
Usage section of ‘.Rd’ files has been removed: such
sections are now ignored (with a warning).

package.skeleton()'s deprecated argument
namespace has been removed.

Many methods are no longer exported by package stats.
They are all registered on their generic, which should be called
rather than calling a method directly.

Functions readNEWS() and checkNEWS() in
package tools are defunct.

download.file(method = "lynx") is deprecated.

.C(DUP = FALSE) and .Fortran(DUP = FALSE) are
now deprecated, and may be disabled in future versions of R. As
their help has long said, .Call() is much preferred.

R CMD check notes such usages (by default).

The workaround of setting R_OSX_VALGRIND has been
removed: it is not needed in current valgrind.

BUG FIXES

Calling lm.wfit() with no non-zero weights gave an
array-overrun in the Fortran code and a not very sensible answer.
It is now special-cased with a simpler answer (no qr
component).

Error messages involving non-syntactic names (e.g., as produced
by `\r` when that object does not exist) now encode
the control characters. (Reported by Hadley Wickham.)

getGraphicsEvent() caused 100% usage of one CPU in
Windows. (PR#15500)

nls() with no start argument may now work
inside another function (scoping issue).

pbeta() and similar work better for very large
(billions) ncp.

Where time zones have changed abbreviations over the years,
the software tries to more consistently use the abbreviation
appropriate to the time or if that is unknown, the current
abbreviation. On some platforms where the C function
localtime changed the tzname variables the reported
abbreviation could have been that of the last time converted.

NOTE for anyone poking around within the graphics engine display
list (despite the warnings not to) that this changes what
is recorded by grid on the graphics engine display list.

Extra checks have been added for unit resolution and
conversion in grid, to catch instances of division-by-zero.
This may introduce error messages in existing code and/or produce
a different result in existing code (but only where a non-finite
location or dimension may now become zero).

Some bugs in TRE have been corrected by updating from the
git repository. This allows R to be installed on some
platforms for which this was a blocker (PR#15087 suggests Linux
on ARM and HP-UX).

? applied to a call to an S4 generic failed in
several cases. (PR#15680)

The implicit S4 generics for primitives with ... in
their argument list were incorrect. (PR#15690)

write.table() now handles matrices of
2^31 or more elements, for those with large amounts
of patience and disc space.

There is a new function, La_version(), to report the
version of LAPACK in use.

The HTML version of ‘An Introduction to R’ now has
links to PNG versions of the figures.

There is some support to produce manuals in ebook
formats. (See ‘doc/manual/Makefile’. Suggested by Mauro
Cavalcanti.)

On a Unix-alike Sys.timezone() returns NA if
the environment variable TZ is unset, to distinguish it from
an empty string which on some OSes means the UTC time zone.

The backtick may now be escaped in strings, to allow names
containing them to be constructed, e.g. `\``. (PR#15621)

read.table(), readLines() and scan()
now warn when an embedded nul is found in the input. (Related to
PR#15625 which was puzzled by the behaviour in this unsupported
case.)

(Windows only.) file.symlink() works around the
undocumented restriction of the Windows system call to
backslashes. (Wish of PR#15631.)

KalmanForecast(fast = FALSE) is now the default, and
the help contains an example of how fast = TRUE can be used
in this version. (The usage will change in 3.1.0.)

strptime() now checks the locale only when
locale-specific formats are used and caches the locale in use:
this can halve the time taken on OSes with slow system
functions (e.g., OS X).

strptime() and the format() methods for
classes "POSIXct", "POSIXlt" and "Date"
recognize strings with marked encodings: this allows, for example,
UTF-8 French month names to be read on (French) Windows.

iconv(to = "utf8") is now accepted on all platforms
(some implementations did already, but GNU libiconv did not:
however converted strings were not marked as being in UTF-8). The
official name, "UTF-8" is still preferred.

Finalizers are marked to be run at garbage collection, but
run only at a somewhat safer later time (when interrupts are
checked). This circumvents some problems with finalizers running
arbitrary code during garbage collection (the known instances being
running options() and (C-level) path.expand()
re-entrantly).

INSTALLATION and INCLUDED SOFTWARE

The included version of PCRE has been updated to 8.34. This
fixes bugs and makes the behaviour closer to Perl 5.18. In
particular, the concept of ‘space’ includes VT and
hence agrees with POSIX's.

PACKAGE INSTALLATION

The new field SysDataCompression in the
‘DESCRIPTION’ file allows user control over the compression
used for ‘sysdata.rda’ objects in the lazy-load database.

(Windows only) When a call to system2() specified
one of stdin, stdout or stderr to be a file,
but the command was not found (e.g., it contained its arguments,
or the program was not on the PATH), it left the file open
and unusable until R terminated. (Reported by Mathew McLean.)

The bmp() device was not recording res = NA
correctly: it is now recorded as 72 ppi.

Several potential problems with compiler-specific behaviour
have been identified using the ‘Undefined Behaviour
Sanitizer’ in conjunction with the clang compiler.

hcl() now honours NA inputs (previously they
were mapped to black).

Some translations in base packages were being looked up in
the main catalog rather than that for the package.

As a result of the 3.0.2 change about ‘the last
second before the epoch’, most conversions which should have given
NA returned that time. (The platforms affected include
Linux and OS X, but not Windows nor Solaris.)

rowsum() has more support for matrices and data frames
with 2^31 or more elements. (PR#15587)

The bug fix in 3.0.2 for PR#15411 was too aggressive,
and sometimes removed spaces that should not have been removed.
(PR#15583)

Running R code in a tcltk callback failed to set the
busy flag, which will be needed to tell OS X not to ‘App Nap’.

The code for date-times before 1902 assumed that the offset
from GMT in 1902 was a whole number of minutes: that was not true
of Paris (as recorded on some platforms).

Using Sys.setlocale to set LC_NUMERIC to
"C" (to restore the sane behavior) no longer gives a
warning.

deparse() now deparses complex vectors in a way that
re-parses to the original values. (PR#15534, patch based on code
submitted by Alex Bertram.)

In some extreme cases (more than 10^15)
integer inputs to dpqrxxx() functions might have been
rounded up by one (with a warning about being non-integer).
(PR#15624)

Plotting symbol pch = 14 had the triangle upside down
on some devices (typically screen devices). The triangle is
supposed to be point up. (Reported by Bill Venables.)

getSrcref() did not work on method definitions if
rematchDefinition() had been used.

KalmanForecast(fast = FALSE) reported a (harmless)
stack imbalance.

The count of observations used by KalmanRun() did not
take missing values into account.

In locales where the abbreviated name of one month is a
partial match for the full name of a later one, the %B
format in strptime() could fail. An example was French on
OS X, where juin is abbreviated to jui and partially
matches juillet. Similarly for weekday names.

pbeta(x, a, b, log.p = TRUE) sometimes underflowed to
zero for very small and very differently sized a, b.
(PR#15641)

approx() and approxfun() now handle infinite
values with the "constant" method. (PR#15655)

stripchart() again respects reversed limits in
xlim and ylim. (PR#15664)

CHANGES IN R 3.0.2

NEW FEATURES

The ‘NEWS’ files have been re-organized.

This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
and 2.x.y releases is in files ‘NEWS.0’, ‘NEWS.1’ and
‘NEWS.2’. The latter files are now installed when R is
installed. An HTML version of news from 2.10.0 to 2.15.3 is
available as ‘doc/html/NEWS.2.html’.

sum() for integer arguments now uses an integer
accumulator of at least 64 bits and so will be more accurate in
the very rare case that a cumulative sum exceeds
2^53 (necessarily summing more than 4 million
elements).

The example() and tools::Rd2ex() functions now
have parameters to allow them to ignore \dontrun markup in
examples. (Suggested by Peter Solymos.)

str(x) is considerably faster for very large lists,
or factors with 100,000 levels, the latter as in PR#15337.

col2rgb() now converts factors to character strings
not integer codes (suggested by Bryan Hanson).

tail(warnings()) now works, via the new
`[` method.

There is now support for the LaTeX style file ‘zi4.sty’
which has in some distributions replaced ‘inconsolata.sty’.

unlist(x) now typically returns all non-list
xs unchanged, not just the “vector” ones.
Consequently, format(lst) now also works when the list
lst has non-vector elements.

The tools::getVignetteInfo() function has been added
to give information about installed vignettes.

Various functions in stats and elsewhere that use
non-standard evaluation are now more careful to follow the
namespace scoping rules. E.g., stats::lm() can now find
stats::model.frame() even if stats is not on the
search path or if some package defines a function of that name.

If an invalid/corrupt .Random.seed object is
encountered in the workspace it is ignored with a warning rather
than giving an error. (This allows R itself to rely on a working
RNG, e.g. to choose a random port.)

seq() and seq.int() give more explicit error
messages if called with invalid (e.g., NaN) inputs.

When parse() finds a syntax error, it now makes
partial parse information available up to the location of the
error. (Request of Reijo Sund.)

Methods invoked by NextMethod() had a different
dynamic parent to the generic. This was causing trouble where S3
methods invoked via lazy evaluation could lose track of
their generic. (PR#15267)

Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.

read.dcf() no longer has a limit of 8191 bytes per
line. (Wish of PR#15250.)

formatC(x) no longer copies the class of x to
the result, to avoid misuse creating invalid objects as in
PR#15303. A warning is given if a class is discarded.

Dataset npk has been copied from MASS to
allow more tests to be run without recommended packages being
installed.

The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been
changed and in some examples avoids a local maximum. (PR#15396)

termplot() now has an argument transform.x
to control the display of individual terms in the plot.
(PR#15329)

format() now supports digits = 0, to
display nsmall decimal places.

There is a new read-only par() parameter called
"page", which returns a logical value indicating whether
the next plot.new() call will start a new page.

Processing Sweave and Rd documents to PDF now renders
backticks and single quotes better in several instances, including
in \code and \samp expressions.

utils::modifyList() gets a new argument keep.null
allowing NULL components in the replacement to be retained,
instead of causing corresponding components to be deleted.

tools::pkgVignettes() gains argument check;
if set to TRUE, it will warn when it appears a vignette requests
a non-existent vignette engine.

UTILITIES

R CMD check --as-cran checks the line widths in
usage and examples sections of the package Rd files.

R CMD check --as-cran now implies --timings.

R CMD check looks for command gfile if a
suitable file is not found. (Although file is
not from GNU, OpenCSW on Solaris installs it as gfile.)

R CMD build (with the internal tar) checks
the permissions of ‘configure’ and ‘cleanup’ files and
adds execute permission to the recorded permissions for these
files if needed, with a warning. This is useful on OSes and file
systems which do not support execute permissions (notably, on
Windows).

R CMD build now weaves and tangles all vignettes,
so suggested packages are not required during package installation
if the source tarball was prepared with current
R CMD build.

checkFF() (used by R CMD check) does a
better job of detecting calls from other packages, including not
reporting those where a function has been copied from another
namespace (e.g., as a default method). It now reports calls where
.NAME is a symbol registered in another package.

On Unix-alike systems, R CMD INSTALL now installs packages
group writably whenever the library (lib.loc) is group
writable. Hence, update.packages() works for other group
members (suggested originally and from a patch by Dirk Eddelbuettel).

R CMD javareconf now supports the use of symbolic
links for JAVA_HOME on platforms which have
realpath. So it is now possible to
use

R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0

on a Linux system and record that value rather than the
frequently-changing full path such as
‘/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64’.

R CMD check does more thorough checking of
declared packages and namespaces. It reports

packages declared in more than one of the
Depends, Imports, Suggests and
Enhances fields of the ‘DESCRIPTION’ file.

namespaces declared in Imports but not
imported from, neither in the ‘NAMESPACE’ file nor using
the :: nor ::: operators.

packages which are used in library() or
requires() calls in the R code but were already put on
the search path viaDepends.

packages declared in Depends not imported
via the ‘NAMESPACE’ file (except the standard
packages). Objects used from Depends packages should be
imported to avoid conflicts and to allow correct operation when
the namespace is loaded but not attached.

objects imported via::: calls where
:: would do.

objects imported by :: which are not exported.

objects imported by ::: calls which do not exist.

See ‘Writing R Extensions’ for good practice.

R CMD check optionally checks for non-standard
top-level files and directories (which are often mistakes): this
is enabled for --as-cran.

LaTeX style file upquote.sty is no longer included
(the version was several years old): it is no longer used in R.
A much later version is commonly included in LaTeX distributions
but does not play well with the ae fonts which are the
default for Sweave vignettes.

R CMD build makes more use of the ‘build’
sub-directory of package sources, for example to record
information about the vignettes.

R CMD check analyses ::: calls.

INSTALLATION and INCLUDED SOFTWARE

The macros used for the texinfo manuals have been changed to
work better with the incompatible changes made in texinfo
5.x.

The minimum version for a system xz library is now
5.0.3 (was 4.999). This is in part to avoid 5.0.2, which can
compress in ways other versions cannot decompress.

The included version of PCRE has been updated to 8.33.

The included version of zlib has been updated to
1.2.8, a bug-fix release.

The included version of xz utils's liblzma has been
updated to 5.0.5.

Since javareconf (see above) is used when R is
installed, a stable link for JAVA_HOME can be supplied then.

Configuring with --disable-byte-compilation will
override the ‘DESCRIPTION’ files of recommended packages,
which typically require byte-compilation.

More of the installation and checking process will work even
when TMPDIR is set to a path containing spaces, but this is
not recommended and external software (such as
texi2dvi) may fail.

PACKAGE INSTALLATION

Installation is aborted immediately if a LinkingTo
package is not installed.

R CMD INSTALL has a new option
--no-byte-compile which will override a ByteCompile
field in the package's ‘DESCRIPTION’ file.

License BSD is deprecated: use BSD_3_clause
or BSD_2_clause instead.

License X11 is deprecated: use MIT or
BSD_2_clause instead.

Version requirements for LinkingTo packages are now
recognized: they are checked at installation. (Fields with
version requirements were previously silently ignored.)

The limit of 500 S3method entries in a
NAMESPACE file has been removed.

The default ‘version’ of Bioconductor for its
packages has been changed to the upcoming 2.13, but this
can be set by the environment variable R_BIOC_VERSION when
R is installed.

C-LEVEL FACILITIES

‘Rdefines.h’ has been tweaked so it can be included in
C++ code after ‘R_ext/Boolean.h’ (which is included by
‘R.h’).

Note that ‘Rdefines.h’ is not kept up-to-date, and
‘Rinternals.h’ is preferred for new code.

eval and applyClosure are now protected
against package code supplying an invalid rho.

DEPRECATED AND DEFUNCT

The unused namespace argument to
package.skeleton() is now formally deprecated and will be
removed in R 3.1.0.

plclust() is deprecated: use the plot() method
for class "hclust" instead.

Functions readNEWS() and checkNEWS() in
package tools are deprecated (and they have not worked with
current ‘NEWS’ files for a long time).

DOCUMENTATION

‘An Introduction to R’ has a new chapter on using R
as a scripting language including interacting with the OS.

BUG FIXES

help.request() could not determine the current version
of R on CRAN. (PR#15241)

On Windows, file.info() failed on root directories unless
the path was terminated with an explicit ".". (PR#15302)

The help for setClass() and
representation() still suggested the deprecated argument
representation=. (PR#15312)

R CMD config failed in an installed build of R
3.0.1 (only) when a sub-architecture was used. (Reported by
Berwin Turlach.)

On Windows, the installer modified the ‘etc/Rconsole’
and ‘etc/Rprofile.site’ files even when default options were
chosen, so the MD5 sums did not refer to the installed versions.
(Reported by Tal Galili.)

If multiple packages were checked by R CMD check,
and one was written for a different OS, it would set
--no-install for all following packages as well as
itself.

qr.coef() and related functions did not properly coerce
real vectors to complex when necessary. (PR#15332)

ftable(a) now fixes up empty dimnames such
that the result is printable.

package.skeleton() was not starting its search for
function objects in the correct place if environment was
supplied. (Reported by Karl Forner.)

Parsing code was changing the length field of vectors and
confusing the memory manager. (PR#15345)

The Fortran routine ZHER2K in the reference BLAS
had a comment-out bug in two places.
This caused trouble with eigen() for Hermitian matrices.
(PR#15345 and report from Robin Hankin)

vignette() and browseVignettes() did not
display non-Sweave vignettes properly.

Two warning/error messages have been corrected:
the (optional) warning produced by a partial name match
with a pairlist, the error message from a zero-length argument to
the : operator. (Found by Radford Neal; PR#15358,
PR#15356)

svd() returned NULL rather than omitting
components as documented. (Found by Radford Neal; PR#15360)

mclapply() and mcparallel() with
silent = TRUE could break a process that uses
stdout output
unguarded against broken pipes (e.g., zip will fail
silently). To work around such issues, they now replace
stdout with a descriptor pointed to ‘/dev/null’
instead. For this purpose, internal closeStdout and
closeStderr functions have gained the to.null flag.

log(), signif() and round() now raise an
error if a single named argument is not named x. (PR#15361)

deparse() now deparses raw vectors in a form that
is syntactically correct. (PR#15369)

The jpeg driver in Sweave created a JPEG file, but gave
it a ‘.png’ extension. (PR#15370)

Deparsing of infix operators with named arguments is
improved. (PR#15350)

system() and system2() are better protected
against users who misguidedly have spaces in the temporary
directory path.

file.show() and edit() are now more likely to
work on file paths containing spaces. (Where external utilities
are used, not the norm on Windows nor in R.app which
should previously have worked.)

Packages using the methods package are more likely to
work when they import it but it is not attached. (Several parts
of its C code were looking for its R functions on the search path
rather than in its namespace.)

lgamma(-x) is no longer NaN for very small x.

(Windows) system2() now respects specifying
stdout and stderr as files if called from
Rgui. (PR#15393)

Closing an x11() device whilst locator() or
identify() is in progress no longer hangs R. (PR#15253)

CHANGES IN R 3.0.1

NEW FEATURES

mcparallel has a new argument mc.interactive
which can modify the interactive flag in the child process. The
new default is FALSE which makes child processes
non-interactive by default (this prevents lock-ups due to children
waiting for interactive input).

scan() now warns when end-of-file occurs within
a quoted string.

count.fields() is now consistent with scan()
in its handling of newlines in quoted strings. Instead of
triggering an error, this results in the current line receiving
NA as the field count, with the next line getting the total
count of the two lines.

The default method of image() will plot axes of the
class of xlim and ylim (and hence of x and
y if there is a suitable range() method). Based on
a suggestion of Michael Sumner.

load() now has a verbose argument for
debugging support, to print the names of objects just before
loading them.

When loading a serialized object encounters a reference to a
namespace which cannot be loaded, this is replaced by a reference
to the global environment, with a warning.

pairs() gains a line.main option for title placement.

The remaining instances in which serialization to a raw
vector was limited to 2GB have been unlimited on a 64-bit
platform, and in most cases serialization to a vector of more than
1GB will be substantially faster.

UTILITIES

R CMD config now make use of personal
‘Makevars’ files under ‘~/.R’ and a site file
‘Makevars.site’, in the same way as R CMD SHLIB and
R CMD INSTALL. This makes the utility more useful in
package configure scripts.

On Windows finding the personal files may require the environment
variable HOME set.

The old behaviour can be obtained with the new options
--no-user-files and --no-site-files.

PACKAGE INSTALLATION

Alternatives to the site and user customization files
‘Makevars.site’ and ‘~/.R/Makevars’ can be specified
via the environment variables R_MAKEVARS_SITE and
R_MAKEVARS_USER respectively. These can be used to suppress
the use of the default files by setting an empty value (where
possible) or a non-existent path.

BUG FIXES

sys.source() did not report error locations when
keep.source = TRUE.

as.POSIXct.numeric was coercing origin using
the tz argument and not "GMT" as documented
(PR#14973).

The active binding to assign fields in reference classes
has been cleaned up to reduce dependence on the class' package
environment, also fixing bug in initializing read-only fields
(inspired by a report from Hadley Wickham).

Profiling of built-in functions with line.profiling=
TRUE did not record the line from which they were called.

citation(pkg) dropped the header and footer specified
in the ‘CITATION’ file (PR#15257).

Quotes were handled differently when reading the first line
and reading the rest, so read.table() misread some files
that contained quote characters (PR#15245).

cat() with sep a character vector of length
greater than one and more than one argument was using separators
inconsistently (PR#15261).

On Windows in R 3.0.0, savePlot() failed because of
an incorrect check on the argument count.

unzip(list = TRUE) returned Names as a factor
and not a character vector (as documented) for the internal method.
(Noticed by Sean O'Riordain.)

contourLines() now checks more comprehensively for
conformance of its x, y and z arguments (it
was used incorrectly in package R2G2).

Saved graphics display lists are R version-specific.
Attempting to load workspaces containing them (or some other
version-specific objects) aborted the load in R 3.0.0 and
earlier; now it does a partial load and generates a warning
instead.

In R 3.0.0, identify() and locator() did
not record information correctly, so replaying a graph (e.g., by
copying it to another device) would fail. (PR#15271)

Calling file.copy() or dirname() with the
invalid input "" (which was being used in packages, despite
not being a file path) could have caused a segfault.

dirname("") is now "" rather than "." (unless
it segfaulted).

supsmu() could read/write outside its input vectors
for very short inputs (seen in package rms for n = 4).

The return value when all workers failed from
parallel::mclapply(mc.preschedule = TRUE) was a list of
strings and not of error objects. (Spotted by Karl Forner and
Bernd Bischl.)

In R 3.0.0, when help() found multiple pages with
the same alias, the HTML display of all the selections was not
produced. (PR#15282)

splinefun(method="monoH.FC") now produces a
function with first argument named x and allows
deriv=3, as documented. (PR#15273)

summaryRprof() would only read the first
chunksize lines of an Rprof file produced with
line.profiling=TRUE. By default, this is the first 100
seconds. (PR#15288)

lsfit() produced an incorrect error message when
argument x had more columns than rows or x had a
different number of rows than y. (Spotted by Renaud Gaujoux.)

Binary operations on equal length vectors copied the
class name from the second operand when the first had no
class name, but did not set the object bit. (PR#15299)

The trace() method for reference generator objects
failed after those objects became function definitions.

write.table() did not check that factors were
constructed correctly, and so caused a segment fault when
writing bad ones. (PR#15300)

The internal HTTP server no longer chokes on POST requests
without body. It will also pass-through other request types for
custom handlers (with the method stored in Request-Method header)
instead of failing.

CHANGES IN R 3.0.0

SIGNIFICANT USER-VISIBLE CHANGES

Packages need to be (re-)installed under this version
(3.0.0) of R.

There is a subtle change in behaviour for numeric index
values 2^31 and larger. These never used to be
legitimate and so were treated as NA, sometimes with a
warning. They are now legal for long vectors so there is no
longer a warning, and x[2^31] <- y will now extend the
vector on a 64-bit platform and give an error on a 32-bit one.

It is now possible for 64-bit builds to allocate amounts of
memory limited only by the OS. It may be wise to use OS
facilities (e.g., ulimit in a bash shell,
limit in csh), to set limits on overall memory
consumption of an R process, particularly in a multi-user
environment. A number of packages need a limit of at least 4GB of
virtual memory to load.

64-bit Windows builds of R are by default limited in memory usage
to the amount of RAM installed: this limit can be changed by
command-line option --max-mem-size or setting environment
variable R_MAX_MEM_SIZE.

Negative numbers for colours are consistently an error:
previously they were sometimes taken as transparent, sometimes
mapped into the current palette and sometimes an error.

NEW FEATURES

identical() has a new argument,
ignore.environment, used when comparing functions (with
default FALSE as before).

There is a new option, options(CBoundsCheck=), which
controls how .C() and .Fortran() pass arguments to
compiled code. If true (which can be enabled by setting the
environment variable R_C_BOUNDS_CHECK to yes), raw,
integer, double and complex arguments are always copied, and
checked for writing off either end of the array on return from the
compiled code (when a second copy is made). This also checks
individual elements of character vectors passed to .C().

This is not intended for routine use, but can be very helpful in
finding segfaults in package code.

In layout(), the limits on the grid size have been
raised (again).

New simple provideDimnames() utility function.

Where methods for length() return a double value
which is representable as an integer (as often happens for package
Matrix), this is converted to an integer.

Matrix indexing of data frames by two-column numeric indices
is now supported for replacement as well as extraction.

setNames() now has a default for its object
argument, useful for a character result.

StructTS() has a revised additive constant in the
loglik component of the result: the previous definition is
returned as the loglik0 component. However, the help page has
always warned of a lack of comparability of log-likelihoods for
non-stationary models. (Suggested by Jouni Helske.)

The logic in aggregate.formula() has been revised.
It is now possible to use a formula stored in a variable;
previously, it had to be given explicitly in the function call.

install.packages() has a new argument quiet to
reduce the amount of output shown.

Setting an element of the graphics argument lwd to a
negative or infinite value is now an error. Lines corresponding
to elements with values NA or NaN are silently
omitted.

Previously the behaviour was device-dependent.

Setting graphical parameters cex, col,
lty, lwd and pch in par() now requires a
length-one argument. Previously some silently took the first
element of a longer vector, but not always when documented to do so.

Sys.which() when used with inputs which would be
unsafe in a shell (e.g., absolute paths containing spaces) now uses
appropriate quoting.

as.tclObj() has been extended to handle raw vectors.
Previously, it only worked in the other direction.
(Contributed by Charlie Friedemann, PR#14939.)

New functions cite() and citeNatbib() have
been added, to allow generation of in-text citations from
"bibentry" objects. A cite() function may be added
to bibstyle() environments.

A sort() method has been added for "bibentry"
objects.

The bibstyle() function now defaults to setting the
default bibliography style. The getBibstyle() function
has been added to report the name of the current default style.

scatter.smooth() now has an argument lpars to
pass arguments to lines().

pairs() has a new log argument, to allow some
or all variables to be plotted on logarithmic scale.
(In part, wish of PR#14919.)

split() gains a sep argument.

termplot() does a better job when given a model with
interactions (and no longer attempts to plot interaction terms).

The parser now incorporates code from Romain Francois'
parser package, to support more detailed computation on
the code, such as syntax highlighting, comment-based
documentation, etc. Functions getParseData() and
getParseText() access the data.

There is a new function rep_len() analogous to
rep.int() for when speed is required (and names are not).

demo() gains an encoding argument for those
packages with non-ASCII demos: it defaults to the package encoding
where there is one.

strwrap() converts inputs with a marked encoding to
the current locale: previously it made some attempt to pass
through as bytes inputs invalid in the current locale.

Specifying both rate and scale to
[dpqr]gamma is a warning (if they are essentially the same
value) or an error.

merge() works in more cases where the data frames
include matrices. (Wish of PR#14974.)

optimize() and uniroot() no longer use a
shared parameter object across calls. (nlm(),
nlminb() and optim() with numerical derivatives
still do, as documented.)

The all.equal() method for date-times is now
documented: times are regarded as equal (by default) if they
differ by up to 1 msec.

duplicated() and unique() gain a nmax
argument which can be used to make them much more efficient when
it is known that there are only a small number of unique entries.
This is done automatically for factors.

sort(), sort.int() and sort.list() now
use radix sorting for factors of less than 100,000 levels when
method is not supplied. So does order() if called
with a single factor, unless na.last = NA.

diag() as used to generate a diagonal matrix has been
re-written in C for speed and less memory usage. It now forces
the result to be numeric in the case diag(x) since it is
said to have ‘zero off-diagonal entries’.

backsolve() (and forwardsolve()) are now
internal functions, for speed and support for large matrices.

sample.int() has some support for n >= 2^31: see its help for the limitations.

A different algorithm is used for (n, size, replace = FALSE,
prob = NULL) for n > 1e7 and size <= n/2. This
is much faster and uses less memory, but does give different results.

approxfun() and splinefun() now return a
wrapper to an internal function in the stats namespace
rather than a .C() or .Call() call. This is more
likely to work if the function is saved and used in a different
session.

The functions .C(), .Call(),
.External() and .Fortran() now give an error (rather
than a warning) if called with a named first argument.

Sweave() by default now reports the locations in
the source file(s) of each chunk.

clearPushBack() is now a documented interface to a
long-existing internal call.

aspell() gains filters for R code, Debian Control
Format and message catalog files, and support for R level
dictionaries. In addition, package utils now provides
functions aspell_package_R_files() and
aspell_package_C_files() for spell checking R and C level
message strings in packages.

bibentry() gains some support for “incomplete”
entries with a crossref field.

gray() and gray.colors() finally allow
alpha to be specified.

monthplot() gains parameters to control the look of
the reference lines. (Suggestion of Ian McLeod.)

Added support for new %~% relation
(“is distributed as”) in plotmath.

domain = NA is accepted by gettext() and
ngettext(), analogously to stop() etc.

termplot() gains a new argument plot = FALSE
which returns information to allow the plots to be modified for
use as part of other plots, but does not plot them.
(Contributed by Terry Therneau, PR#15076.)

quartz.save(), formerly an undocumented part of
R.app, is now available to copy a device to a
quartz() device. dev.copy2pdf() optionally does
this for PDF output: quartz.save() defaults to PNG.

The default method of pairs() now allows
text.panel = NULL and the use of <foo>.panel = NULL
is now documented.

setRefClass() and getRefClass() now return
class generator functions, similar to setClass(), but
still with the reference fields and methods as before
(suggestion of Romain Francois).

New functions bitwNot(), bitwAnd(),
bitwOr() and bitwXor(), using the internal
interfaces previously used for classes "octmode" and
"hexmode".

Also bitwShiftL() and bitwShiftR() for shifting bits
in elements of integer vectors.

New option "deparse.cutoff" to control the deparsing
of language objects such as calls and formulae when printing.
(Suggested by a comment of Sarah Goslee.)

colors() gains an argument distinct.

New demo(colors) and demo(hclColors), with
utility functions.

list.files() (aka dir()) gains a new optional
argument no.. which allows to exclude "." and
".." from listings.

Multiple time series are also of class "matrix";
consequently, head(), e.g., is more useful.

encodeString() preserves UTF-8 marked encodings.
Thus if factor levels are marked as UTF-8 an attempt is made to
print them in UTF-8 in RGui on Windows.

readLines() and scan() (and hence
read.table()) in a UTF-8 locale now discard a UTF-8
byte-order-mark (BOM). Such BOMs are allowed but not recommended
by the Unicode Standard: however Microsoft applications can
produce them and so they are sometimes found on websites.

The encoding name "UTF-8-BOM" for a connection will
ensure that a UTF-8 BOM is discarded.

mapply(FUN, a1, ..) now also works when a1 (or
a further such argument) needs a length() method (which the
documented arguments never do). (Requested by Hervé Pagès; with a
patch.)

.onDetach() is supported as an alternative to
.Last.lib. Unlike .Last.lib, this does not need to
be exported from the package's namespace.

The srcfile argument to parse() may now be a
character string, to be used in error messages.

loadNamespace() allows a version specification to be
given, and this is used to check version specifications given in
the Imports field when a namespace is loaded.

setClass() has a new argument, slots, clearer
and less ambiguous than representation. It is recommended
for future code, but should be back-compatible. At the same time,
the allowed slot specification is slightly more general. See the
documentation for details.

mget() now has a default for envir (the frame
from which it is called), for consistency with get() and
assign().

close() now returns an integer status where available,
invisibly. (Wish of PR#15088.)

The internal method of tar() can now store paths too
long for the ustar format, using the (widely supported) GNU
extension. It can also store long link names, but these are much
less widely supported. There is support for larger files, up to
the ustar limit of 8GB.

Local reference classes have been added to package
methods. These are a technique for avoiding unneeded
copying of large components of objects while retaining standard R
functional behavior. See ?LocalReferenceClasses.

untar() has a new argument restore_times which
if false (not the default) discards the times in the tarball.
This is useful if they are incorrect (some tarballs submitted to
CRAN have times in a local time zone or many years in the
past even though the standard required them to be in UTC).

replayplot() cannot (and will not attempt to) replay
plots recorded under R < 3.0.0. It may crash the R session if
an attempt is made to replay plots created in a different build of
R >= 3.0.0.

Palette changes get recorded on the display list, so
replaying plots (including when resizing screen devices and using
dev.copy()) will work better when the palette is changed
during a plot.

chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.

The parse() function has a new parameter
keep.source, which defaults to options("keep.source").

Profiling viaRprof() now optionally records
information at the statement level, not just the function level.

The Rprof() function now quotes function names in
in its output file on Windows, to be consistent with the quoting
in Unix.

Profiling viaRprof() now optionally records
information about time spent in GC.

The HTML help page for a package now displays non-vignette
documentation files in a more accessible format.

To support options(stringsAsFactors = FALSE),
model.frame(), model.matrix() and
replications() now automatically convert character
vectors to factors without a warning.

Deparsing involving calls to anonymous functions has been
made closer to reversible by the addition of extra parentheses.

The function utils::packageName() has been added as
a lightweight version of methods::getPackageName().

find.package(lib.loc = NULL) now treats loaded
namespaces preferentially in the same way as attached packages
have been for a long time.

In Windows, the Change Directory dialog now defaults to
the current working directory, rather than to the last directory
chosen in that dialog.

available.packages() gains a
"license/restricts_use" filter which retains only packages
for which installation can proceed solely based on packages which
are guaranteed not to restrict use.

New check_packages_in_dir() function in package
tools for conveniently checking source packages along with
their reverse dependencies.

R's completion mechanism has been improved to handle help
requests (starting with a question mark). In particular, help
prefixes are now supported, as well as quoted help topics. To
support this, completion inside quotes are now handled by R by
default on all platforms.

The memory manager now allows the strategy used to balance
garbage collection and memory growth to be controlled by setting
the environment variable R_GC_MEM_GROW. See ?Memory
for more details.

(‘For experts only’, as the introductory manual
says.) The use of environment variables R_NSIZE and
R_VSIZE to control the initial (= minimum) garbage
collection trigger for number of cons cels and size of heap has
been restored: they can be overridden by the command-line options
--min-nsize and --min-vsize; see ?Memory.

On Windows, the device name for bitmap devices as reported
by .Device and .Devices no longer includes the file
name. This is for consistency with other platforms and was
requested by the lattice maintainer.

win.metafile() still uses the file name: the exact form is
used by package tkrplot.

set.seed(NULL) re-initializes .Random.seed as
done at the beginning of the session if not already set.
(Suggestion of Bill Dunlap.)

The breaks argument in hist.default() can now be
a function that returns the breakpoints to be used (previously it
could only return the suggested number of breakpoints).

File ‘share/licenses/licenses.db’ has some
clarifications, especially as to which variants of ‘BSD’
and ‘MIT’ is intended and how to apply them to packages.
The problematic licence ‘Artistic-1.0’ has been removed.

LONG VECTORS

This section applies only to 64-bit platforms.

There is support for vectors longer than 2^31
- 1 elements. This applies to raw, logical, integer, double,
complex and character vectors, as well as lists. (Elements of
character vectors remain limited to 2^31 - 1
bytes.)

Most operations which can sensibly be done with long vectors
work: others may return the error ‘long vectors not
supported yet’. Most of these are because they explicitly work
with integer indices (e.g., anyDuplicated() and
match()) or because other limits (e.g., of character strings
or matrix dimensions) would be exceeded or the operations would be
extremely slow.

length() returns a double for long vectors, and
lengths can be set to 2^31 or more by the
replacement function with a double value.

Most aspects of indexing are available. Generally
double-valued indices can be used to access elements beyond
2^31 - 1.

There is some support for matrices and arrays with each
dimension less than 2^31 but total number of
elements more than that. Only some aspects of matrix algebra work
for such matrices, often taking a very long time. In other cases
the underlying Fortran code has an unstated restriction (as was
found for complex svd()).

dist() can produce dissimilarity objects for more
than 65536 rows (but for example hclust() cannot process
such objects).

serialize() to a raw vector is unlimited in size
(except by resources).

The C-level function R_alloc can now allocate
2^35 or more bytes.

agrep() and grep() will return double vectors
of indices for long vector inputs.

Many calls to .C() have been replaced by
.Call() to allow long vectors to be supported (now or in
the future). Regrettably several packages had copied the non-API
.C() calls and so failed.

.C() and .Fortran() do not accept long vector
inputs. This is a precaution as it is very unlikely that existing
code will have been written to handle long vectors (and the R
wrappers often assume that length(x) is an integer).

Most of the methods for sort() work for long vectors.

rank(), sort.list() and order() support
long vectors (slowly except for radix sorting).

sample() can do uniform sampling from a long vector.

PERFORMANCE IMPROVEMENTS

More use has been made of R objects representing registered
entry points, which is more efficient as the address is provided
by the loader once only when the package is loaded.

This has been done for packages base, methods,
splines and tcltk: it was already in place for the
other standard packages.

Since these entry points are always accessed by the R entry
points they do not need to be in the load table which can be
substantially smaller and hence searched faster. This does mean
that .C / .Fortran / .Call calls copied from
earlier versions of R may no longer work – but they were never
part of the API.

Many .Call() calls in package base have been
migrated to .Internal() calls.

solve() makes fewer copies, especially when b
is a vector rather than a matrix.

eigen() makes fewer copies if the input has dimnames.

Most of the linear algebra functions make fewer copies when
the input(s) are not double (e.g., integer or logical).

A foreign function call (.C() etc) in a package
without a PACKAGE argument will only look in the first DLL
specified in the ‘NAMESPACE’ file of the package rather than
searching all loaded DLLs. A few packages needed PACKAGE
arguments added.

The @<- operator is now implemented as a primitive,
which should reduce some copying of objects when used. Note that
the operator object must now be in package base: do not try
to import it explicitly from package methods.

PACKAGE INSTALLATION

The transitional support for installing packages without
namespaces (required since R 2.14.0) has been removed.
R CMD build will still add a namespace, but a
.First.lib() function will need to be converted.

R CMD INSTALL no longer adds a namespace (so
installation will fail), and a .First.lib() function in a
package will be ignored (with an installation warning for now).

As an exception, packages without a ‘R’ directory and no
‘NAMESPACE’ file can still be installed.

Packages can specify in their ‘DESCRIPTION file’ a line
like

Biarch: yes

to be installed on Windows with --force-biarch.

Package vignettes can now be processed by other engines
besides Sweave; see ‘Writing R Extensions’ and the
tools::vignetteEngine help topic for details.

The ‘*.R’ tangled source code for vignettes is now
included in tarballs when R CMD build is used to produce
them. In R 3.0.0, ‘*.R’ files not in the sources will be
produced at install time, but eventually this will be dropped.

The package type "mac.binary" now looks in a path in
the repository without any Mac subtype (which used to be
universal or leopard): it looks in
‘bin/macosx/contrib/3.0’ rather than
‘bin/macosx/leopard/contrib/2.15’). This is the type used
for the CRAN binary distribution for OS X as from R
3.0.0.

File ‘etc/Makeconf’ makes more use of the macros
$(CC), $(CXX), $(F77) and $(FC), so
the compiler in use can be changed by setting just these (and if
necessary the corresponding flags and FLIBS) in file
‘~/.R/Makevars’.

This is convenient for those working with binary distributions of
R, e.g. on OS X.

UTILITIES

R CMD check now gives a warning rather than a
note if it finds calls to abort, assert or
exit in compiled code, and has been able to find the
‘.o’ file in which the calls occur.

Such calls can terminate the R process which loads the package.

The location of the build and check environment files can
now be specified by the environment variables
R_BUILD_ENVIRON and R_CHECK_ENVIRON, respectively.

R CMD Sweave gains a --compact option
to control possibly reducing the size of the PDF file it creates
when --pdf is given.

R CMD check now does some checks on functions
defined within reference classes, including of .Call() etc
calls.

R CMD check --as-cran notes assignments to the
global environment, calls to data() which load into the
global environment, and calls to attach().

R CMD build by default uses the internal method of
tar() to prepare the tarball. This is more likely to
produce a tarball compatible with R CMD INSTALL and
R CMD check: an external tar program,
including options, can be specified via the environment
variable R_BUILD_TAR.

tools::massageExamples() is better protected against
packages which re-define base functions such as cat() and
get() and so can cause R CMD check to fail when
checking examples.

R CMD javareconf has been enhanced to be more
similar to the code used by configure.

There is now a test that a JNI program can be compiled (like
configure did) and only working settings are used.

It makes use of custom settings from configuration recorded in
‘etc/javaconf’.

The --no-vignettes argument of R CMD
build has been renamed to the more accurate
--no-build-vignettes: its action has always been to
(re)build vignettes and never omitted them.

The keep.source argument to library() and
require() is defunct. This option needs to be set
at install time.

Documentation for real(), as.real() and
is.real() has been moved to ‘defunct’ and the
functions removed.

The maxRasters argument of pdf() (unused since
R 2.14.0) has been removed.

The unused fontsmooth argument has been removed from
the quartz() device.

All the (non-API) EISPACK entry points in R have been removed.

chol(pivot = TRUE, LINPACK = TRUE) is deprecated.

The long-deprecated use of \synopsis in the
Usage section of ‘.Rd’ files will be removed in R
3.1.0.

.find.package() and .path.package() are
deprecated: only the public versions without the dot have ever
been in the API.

In a package's ‘DESCRIPTION’ file,

License: X11

is deprecated, since it includes
‘Copyright (C) 1996 X Consortium’ which cannot be
appropriate for a current R package. Use ‘MIT’ or
‘BSD_2_clause’ instead.

CODE MIGRATION

The C code underlying base graphics has been migrated to the
graphics package (and hence no longer uses
.Internal() calls).

Most of the .Internal() calls used in the stats
package have been migrated to C code in that package.

This means that a number of .Internal() calls which have
been used by packages no longer exist, including
.Internal(cor).Internal(cov),
.Internal(optimhess) and .Internal(update.formula).

Some .External() calls to the base package
(really to the R executable or shared library) have been moved to
more appropriate packages. Packages should not have been using
such calls, but some did (mainly those used by integrate()).

PACKAGE parallel

There is a new function mcaffinity() which allows
getting or setting the CPU affinity mask for the current R process on
systems that supports this (currently only Linux has been tested
successfully). It has no effect on systems which do not support
process affinity. Users are not expected to use this function
directly (with the exception of fixing libraries that break
affinity settings like OpenBLAS) – the function is rather
intended to support affinity control in high-level parallel
functions. In the future, R may supplement lack of affinity
control in the OS by its own bookkeeping viamcaffinity()
related to processes and threads it spawns.

mcparallel() has a new argument mc.affinity
which attempts to set the affinity of the child process according
to the specification contained therein.

The port used by socket clusters is chosen randomly: this
should help to avoid clashes observed when two users of a
multi-user machine try to create a cluster at the same time. To
reproduce the previous behaviour set environment variable
R_PARALLEL_PORT to 10187.

C-LEVEL FACILITIES

There has been some minor re-organization of the non-API
header files. In particular, ‘Rinternals.h’ no longer
includes the non-API header ‘R_exts/PrtUtil.h’, and that no
longer includes ‘R_exts/Print.h’.

Passing NULL to .C() is now an error.

.C() and .Fortran() now warn if
"single" arguments are used with DUP = FALSE, as
changes to such arguments are not returned to the caller.

C entry points R_qsort and R_qsort_I now have
start and end as size_t to allow them to work
with longer vectors on 64-bit platforms. Code using them should
be recompiled.

A few recently added C entry points were missing the
remapping to Rf_, notably [dpq]nbinom_mu.

Some of the interface pointers formerly available only to
R.app are now available to front-ends on all
Unix-alikes: one has been added for the interface to
View().

PACKAGE = "" is now an error in .C() etc calls:
it was always contrary to the documentation.

Entry point rcont2 has been migrated to package
stats and so is no longer available.

R_SVN_REVISION in ‘Rversion.h’ is now an integer
(rather than a string) and hence usable as e.g.
#if R_SVN_REVISION < 70000.

The entry points rgb2hsv and hsv2rgb have been
migrated to package grDevices and so are no longer available.

R_GE_version has been increased to 10 and
name2col removed (use R_GE_str2col instead). R
internal colour codes are now defined using the typedef
rcolor.

The REPROTECT macro now checks that the protect index
is valid.

Several non-API entry points no longer used by R have been
removed, including the Fortran entry points chol,
chol2inv, cg, ch and rg, and the C
entry points Brent_fmin, fft_factor and fft_work.

If a .External call is registered with a number of
arguments (other than -1), the number of arguments passed
is checked for each call (as for other foreign function calls).

It is now possible to write custom connection
implementations outside core R using ‘R_ext/Connections.h’.
Please note that the implementation of connections is still
considered internal and may change in the future (see the above
file for details).

INTERNATIONALIZATION

The management of translations has been converted to R
code: see ?tools::update_pkg_po.

The translations for the R interpreter and
RGui.exe are now part of the base package (rather than
having sources in directory ‘po’ and being installed to
‘share/locale’). Thus the base package supports three
translation domains, R-base, R and RGui.

The compiled translations which ship with R are all
installed to the new package translations for easier
updating. The first package of that name found on
.libPaths() at the start of the R session will be used.
(It is possible messages will be used before .libPaths() is
set up in which case the default translations will be used: set
environment variable R_TRANSLATIONS to point to the location
of the intended translations package to use this right from
the start.)

The translations form a separate group in the Windows
installer, so can be omitted if desired.

The markup for many messages has been changed to make them
easier to translate, incorporating suggestions from Łukasz Daniel.

INSTALLATION

There is again support for building without using the C
‘long double’ type. This is required by C99, but system
implementations can be slow or flawed. Use configure
option --disable-long-double.

make pdf and make install-pdf now make
and install the full reference index (including all base and
recommended packages).

The 'reference manual' on the Windows GUI menu and included
in the installer is now the full reference index, including all
base and recommended packages.

R help pages and manuals have no ISBNs because ISBN
rules no longer allow constantly changing content to be assigned
an ISBN.

The Windows installer no longer installs a Start Menu
link to the static help pages; as most pages are generated
dynamically, this led to a lot of broken links.

Any custom settings for Java configuration are recorded in
file ‘etc/javaconf’ for subsequent use by R CMD
javareconf.

There is now support for makeinfo version 5.0
(which requires a slightly different ‘.texi’ syntax).

The minimum versions for --use-system-zlib and
--use-system-pcre are now tested as 1.2.5 and 8.10
respectively.

On Windows, the stack size is reduced to 16MB on 32-bit
systems: misguided users were launching many threads without
controlling the stack size.

configure no longer looks for file
‘~/.Rconfig’: ‘~/.R/config’ has long been preferred.

BUG FIXES

When R CMD build is run in an encoding other than
the one specified in the package's ‘DESCRIPTION’ file it
tries harder to expand the authors@R field in the specified
encoding. (PR#14958)

If R CMD INSTALL is required to expand the
authors@R field of the ‘DESCRIPTION’ file, it tries
harder to do so in the encoding specified for the package (rather
than using ASCII escapes).

Fix in package grid for pushing a viewport into a
layout cell, where the layout is within a viewport that has zero
physical width OR where the layout has zero total relative width
(likewise for height). The layout column widths (or row heights)
in this case were being calculated with non-finite values.
(Reported by Winston Chang.)

solve(A, b) for a vector b gave the answer
names from colnames(A) for LINPACK = TRUE but not in
the default case.

La.svd() accepts logical matrices (as documented, and
as svd() did).

legend() now accepts negative pch values, in
the same way points() long has.

Parse errors when installing files now correctly display
the name of the file containing the bad code.

In Windows, tcltk windows were not always properly constructed.
(PR#15150)

The internal functions implementing parse(),
tools::parseLatex() and tools::parse_Rd() were not
reentrant, leading to errors in rare circumstances such as a
garbage collection triggering a recursive call.

Field assignments in reference class objects via$<- were not being checked
because the magic incantation to turn methods on for that
primitive operator had been inadvertently omitted.

setHook(hookname, value, action="replace") set the
hook to be the value, rather than a list containing the value as
documented. (PR#15167)

If a package used a ‘NEWS.Rd’ file, the main HTML
package index page did not link to it. (Reported by Dirk
Eddelbuettel.)

The primitive implementation of @<- was not
checking the class of the replacement. It now does a check,
quicker but less general than slot<-. See the help.

split(x, f) now recycles classed objects x in
the same way as vectors. (Reported by Martin Morgan.)